Mewtwo Zwei
by Count Morningstar
Summary: While traveling to Kalos to participate in one of the region's first Pokemon Contests, Dawn's plane crashes in the ocean and she winds up on an island that's home to Dr. Fuji, the scientist who created Mewtwo. During her stay, Dawn discovers that the scientist has not only recreated his experiment, but has made something else too. Takes place after Dusk of the Dead.
1. The Island of Dr Fuji

**Introduction:** I'd like to start off by apologizing to the regular readers of my Pokemon AU. I know I've neglected these stories for far too long, and I wouldn't be surprised if I probably lost a lot of you because of it. The thing is that I just tend to get a little burnt out on writing these Pokemon stories sometimes. Of course part of that had to do with the pace I had set for myself at the time, but there have been times where I'd just get so sick of the whole AU that I'd really want to work on something totally different. For now though, my creative spark for this little AU of mine has returned with all the news of the new Sun and Moon games that have been coming out recently.

I know I still have my _Thunder in Kanto_ story to finish, and I also know that many of you are still waiting for me to work on _Reign of Silver_. I still can't say when I'll finally get Reign of Silver off the ground, but I can assure everyone that I plan to start wrapping up _Thunder in Kanto_ fairly soon. In the meantime, I'd like to present everyone with this new story that I've been working on for the past few days. I've had the concept for this story ever since X and Y came out, but for a long time I had been running into walls with it until just last week. The inspiration behind this story came from the female Mewtwo that appeared in that Genesect movie from the Black and White era.

There are just two other things I'd like to mention before we get into our story. The first is that if anyone reading hasn't read my earlier story, _Dusk of the Dead_ , you should probably go back and do that now. The epilogue to that story is especially important. The other thing is that I kind of ripped off some of the plot elements from the H.G. Wells novel, _The Island of Dr. Moreau_ to use for this story. That said, on with the show.

 **Disclaimer:** I do not own Pokemon.

* * *

Chapter 1: The Island of Dr. Fuji

Dawn Berlitz sat looking out the window of her plane at a sky covered by thick grey clouds. Sitting in the seat next to Dawn was a short penguin-like bird with a large blue head and a light-blue body. It had a short orange beak and large white circles around its eyes, along with two small white circles on the front of its chest. This was Dawn's first Pokemon, Piplup. At that moment, Dawn and Piplup were passengers on a small plane flying across the ocean. The plane was taking them to a city in the Kalos Region where Dawn was going to participate in a Pokemon Contest. Pokemon Contests were starting to become big in the Kalos Region, and Dawn was looking forward to participate in the city's very first one.

It was also Dawn's hope that the contest in Kalos would be a fresh start for her. The fact was that the twenty-two year old coordinator had been having a very rough time. Just over a month ago, Dawn had broken up with her boyfriend from Lavender Town in Kanto after she found out he had been cheating on her with his maid. At that same time, Dawn had also had a very rough reunion with her two sisters, Dusk and Diane. The reunion had been so harsh that Dawn broke her arm during a fight with them that had gotten out of hand. The physical and emotional toll of the whole ordeal had caused Dawn to go back to her hometown in Sinnoh to recover. But now that her cast was finally off, Dawn felt like she wanted to get back out on the road.

Unfortunately, Dawn's new journey had not been getting off to a good start. She had been late getting to the airport and missed her original flight to Kalos, forcing her to negotiate passage on a small plane delivering mail to the region. It had helped that the pilot was a fan of Dawn's mother, the champion coordinator Johanna. Only half way through the flight though, the weather had taken a turn for the worse. As Dawn looked out the window, she could see that they had flown into a storm.

"Uh, hey. Do you think that maybe we should turn back?" Dawn asked the pilot. "It looks pretty rough out there."

"Relax, little lady. I've flown through worse weather than this." The pilot assured her. "Besides, we don't have enough fuel to turn around and go back. We're almost there. Don't worry."

Dawn tried to assure herself that the pilot did indeed know what he was doing. He did appear to be a veteran aviator. Still, the storm seemed to be getting worse and worse by the second. Every now and then she could see a flash of lightning in the distance. Before long, a heavy rain started to come down outside. The wind of the storm had increased too, causing some turbulence that frightened Piplup. Suddenly a blot of lightning hit the wing of the plane, causing the engine on it to catch on fire. The plane began to plummet towards the ocean below. The pilot tried to pull up, but his efforts seemed to be in vein. The aircraft hit the water, and the force of the resulting impact caused Dawn to hit her head on the window. Dawn's world went completely dark as the plane started to sink.

* * *

Dawn slowly opened her eyes, and as he vision came into focus she saw Piplup's face staring down at her. It took the blunette a few moments to recall what had happened. Slowly, Dawn began to sit up and found that she was in a bed in an unfamiliar room. It was fairly small and minimally furnished. The wallpaper was colored a dull yellow, and by the wall to Dawn's left was a large oak dresser with a mirror. Directly in front of the blunette was a wall that had a very large window overlooking a tropical forest. There was an almost equally large window in the wall directly next to Dawn's bed.

Once Dawn had fully set up, a relieved Piplup cuddled up to her chest with tears in his eyes. Dawn responded by smiling and putting an arm around the little penguin Pokemon. She was relieved that Piplup was okay, then suddenly wondered about her other five Pokemon. Dawn looked frantically around the room and was relieved to find all six of her pokeballs sitting on the dresser.

"Good! You're finally awake." A voice suddenly spoke. "I was starting to become as concerned as your little friend was."

Dawn looked and found that the single door to her room was open. In the middle of the doorway was a man in an electric wheelchair. He had grey hair that grew out over his forehead and a curled grey beard. The left side of his face was scared as though it had been burned and he had on a pair of oval framed glasses. The man's outfit consisted of a tan short-sleeved shirt with tan slacks. A black glove covered the wheelchair-bound man's left hand, while his right hand was bare.

"Who are you?" Dawn asked. "And where am I?"

"I am Dr. Fuji." The man answered as he wheeled himself completely into the room. "As for where you are, you're in the guestroom of my house, which is on an island about forty miles of the coast of Kalos. As for how you got here, you and your Piplup washed up on shore. My assistant, Muldoon found you both and brought you back here to the house. Fortunately I had all the equipment here to treat you and your Pokemon."

"Was there anyone else besides me and Piplup on the beach?" Dawn asked, worried about the pilot.

"I'm afraid not." Dr. Fuji answered as he shook his head. "By the way, you might wish to know that you've been unconscious for about three days. I am quite curious to know how you washed up here."

"Piplup and I were on a plane to the Kalos Region when we ended up in a storm." Dawn explained. "Lightning struck one of the wings and we crashed into the water."

"Well, you and your Pokemon are all extremely lucky." Dr. Fuji declared. "It's not very often for me to have visitors here."

"Um… thank you for everything that you've done, but I'd like to get back on my way to Kalos if it's possible." Dawn told him. "Do you have a boat here or something that could take me there?"

"I understand your wish to leave, but I'm afraid it's impossible for you to get off the island at the moment." Dr. Fuji informed her. "There are no boats on this island, or anything else besides this house for that matter. There is a boat that comes by here bringing supplies, but it's not due here for another three weeks. When it does arrive though, I'm sure the captain would be agreeable to giving you a lift to Kalos. Until then, feel free to consider yourself my guest."

"Well, I guess that'll have to do." Dawn replied.

"Muldoon brought you a change of clothes for when you finally woke up." Dr. Fuji told her, pointing at the closet in the wall behind Dawn. "It's not exactly what a young woman your age would consider high fashion, but it should be suitable for your stay here. If you're feeling up to it, you're welcome to join me for dinner in two hours."

"Now that you mention it, I probably could use something to eat." Dawn realized.

"Excellent. I'll tell Muldoon to set a place for you." Dr. Fuji replied. And with that, he left the room.

After a few moments, Dawn got out of bed and changed into one of the outfits that Dr. Fuji's assistant had prepared for her. The closet was filled with fourteen versions of the same outfit: A short-sleeved tan shirt with pockets on the front and tan cargo shorts. Dawn put one of the outfits on, along with the pair of black boots that had been prepared for her. Dawn felt like she was dressing up to go on some kind of jungle expedition. She was at least thankful that she still had her yellow hair barrettes.

Dawn left the room with Piplup when dinnertime finally arrived, and the two of them managed to find their way to the dining room. It was a slightly large rectangular room with a long table designed to seat six people. Dr. Fuji was already at the end of the table and several plates of food had been set out on the white tablecloth.

"Delighted that you could join me." Dr. Fuji told her. "I don't believe that I got your name before."

"Sorry. I'm Dawn Berlitz." The blunette replied as she sat at the other end of the table. Piplup, meanwhile, had quickly waddled over to a bowl of Pokemon food that had been laid out for him in a corner of the room. "Um, will Mr. Muldoon be joining us?"

"No. Muldoon prefers to eat in his quarters." Dr. Fuji answered. "He's a good assistant, but not very sociable. Actually, the more accurate job title for him is manservant, but that term probably isn't very politically correct these days."

Dawn nodded and the two of them began to eat. A heavy silence hung over the room for what seemed like several minutes. It was natural, of course. After all, Dawn didn't know the first thing about her host, and her host had only just learned her name. Plus the good doctor was old enough to be her father or maybe even her grandfather. There was also something peculiar about Dr. Fuji that Dawn could not place, something that she couldn't help but find a little disquieting.

"So Dawn, I'm correct in assuming that you're a Pokemon trainer?" Dr. Fuji asked in an attempt to start up a conversation.

"Pretty much." The blunette confirmed. "Actually, I'm a Pokemon coordinator. I was on my way to a Pokemon Contest in Kalos when my plane crashed."

"Ah yes. I've heard of these Pokemon Contests before." Dr. Fuji recalled. "I've never actually seen one though. I don't pay much attention to the world outside this island."

"I see…" Dawn replied. The awkward silence from before returned for several moments. "So… just what kind of doctor are you anyway?"

"I'm a geneticist." Dr. Fuji answered. "My specialty is cloning."

"You mean like brining back Pokemon from fossils?" Dawn asked.

"I did help to develop that technology, but my attempts at cloning have been more… revolutionary." Dr. Fuji answered. "But I'm sure a young lady like you wouldn't be interested in such things. Besides, it was long ago and I've since retired."

Dawn nodded and looked around the room for something else she could use to start another conversation. Within seconds she spotted the picture of a little girl with long green hair and a big smile on her face hanging on the wall to her left. She had on a sun hat and a white dress.

"Who's the girl in that picture over there?" Dawn asked.

Dr. Fuji looked at the picture Dawn indicated and sighed. "That, Ms. Berlitz, is my daughter… Amber."

"Where is she now?' Dawn asked.

"…She died… many years ago." The good doctor answered. "I never truly got over her death. I coped with it by throwing myself into my work, chasing an impossible dream that I eventually found could never be realized. My work cost me my marriage, and many other things. Now here I am, an old man living alone on an island with nothing but old memories and shattered dreams."

"I'm… sorry to hear that." Dawn responded.

"…I think I'll retire for the evening." Dr. Fuji decided. "I'm sorry that I couldn't be better company to you."

With that, Dr. Fuji wheeled himself out of the room. Dawn continued her meal in silence. She realized she had brought up a sensitive subject for her host and regretted it a bit. After finishing her dinner, Dawn took Piplup and went back to her room.

* * *

It was the dead of night, and Dawn was lying in her bed staring up at the ceiling. Her encounters with Dr. Fuji were keeping her from getting to sleep. There were too many things about the good doctor that Dawn couldn't help but find strange, questions that she couldn't figure out the answers to. Why was Dr. Fuji living alone on some remote island? How did he get those scars covering his body? And just what was sort of work was it that Dr. Fuji did before he retired?

Dawn got out of bed, deciding that she needed to walk around and explore the house to take her mind off things. Plplup woke up as Dawn left the room and quickly followed after her, tripping along the way as he headed for the door. Dawn and Piplup eventually came to a fairly large room that seemed to be some kind of library. There were shelves of books lining each of the walls, and in the center of the room were two green chairs. Between them was a round table made of polished wood, and on top of the table was a lamp with a blue lampshade and a bottle of what appeared to be brandy along with a single empty glass and a brown book with a bookmark sticking out of the middle.

Dawn decided that reading a book might quiet her thoughts and help her get to sleep. She began to peruse the shelves for just the right book. At last she found a book that she thought might do the trick. It was a thick book on the history of the Kalos Region, interesting yet at the same time boring enough to make her drowsy enough to go to sleep. When Dawn tried to pull out the book, the entire shelf suddenly retracted into the wall. A startled Piplup hid behind Dawn's legs as the bookcase move aside after retracting into the wall, revealing an opening to a hidden room. The opening was completely dark except for electronic lights that Dawn thought might be from pieces of computer equipment.

Against her better judgment, Dawn decided to go through the opening and investigate. Piplup hung back for a moment out of fear before quickly following after Dawn, deciding that being alone might be more dangerous than going in. The chamber beyond the opening seemed quite large, but it was hard for Dawn to tell exactly what was inside because it was so dark. Suddenly a pair of lights clicked on as soon as Dawn took at few more steps in. The lights were coming from a pair of glass tubes. Dawn took a look at the first tube before her and was completely stunned by what she saw.

Floating inside the tube, which seemed to contain some kind of odd yellow liquid, was a young woman who appeared to be in her early twenties. She had long green hair and was in a fetal position, completely naked except for some kind of device that seemed to be covering her eyes. The machine had thick black wires leading from it to the bottom of the tube. Dawn suspected that the wires were connected to the computers at the back of the room but couldn't be sure. As Dawn looked at the young woman in the tube, Piplup looked at the other tube giving off light and alerted Dawn with a startled cry.

Dawn looked at the other tube and saw that it was not only full of the same yellow liquid as the one containing the girl, but that it was also occupied. The thing inside the second tube was a six-foot-tall bipedal feline that was purplish-grey in color. Its stomach and tail were purple and it had a cord-like growth on the back of its neck. The creature's eyes were closed as if asleep. Dawn had encountered the Pokemon in the tube once before. She had run into it back in Lavender Town a month ago when she had her little fight with her sisters. It was Mewtwo.

* * *

 **Author's Note:** The main reason why Dawn is the hero of this story is because I just wanted to use her in another story. I rather like Dawn. I don't like her as a love interest for Ash, but she is one of the better characters from the anime. Anyway, the next chapter is already up, so go ahead and take a look.

If you'd like, please review and let me know what you think.


	2. Amber Drei

**Disclaimer:** I do not own Pokemon.

* * *

Chapter 2: Amber Drei

Dawn was trying to wrap her head around just what it was she had stumbled upon. It was as if she had walked into some kind of chamber of horrors. She knew that Dr. Fuji was a scientist, but she had no idea that he was running such twisted experiments. Dawn recalled what little her friend, Ash Ketchum had told her about Mewtwo and how that he was a Pokemon created by science, but that didn't explain just how the psychic feline had ended up in a tube in some secret lab. Nor did it explain the identity of the young woman floating in the other tube of liquid.

"It seems that someone let their curiosity get the better of them." A voice spoke, causing Dawn to jump. Dawn saw that it was Dr. Fuji.

"What… what the hell is all this?" a frightened Dawn asked. "Who's that girl? And how… how did Mewtwo end up in that tube? What did you do to him?"

"Mewtwo? I see… so you've heard of my creation." Dr. Fuji realized.

"Your… creation?" Dawn asked.

"I mentioned to you before, Ms. Berlitz that I specialized in cloning." Dr. Fuji continued as he wheeled his chair closer to Dawn. "Mewtwo was my ultimate achievement. I had set out to create the world's strongest Pokemon, using the DNA the legendary Pokemon, Mew as a base. Mew is a genetically perfect life form capable of learning almost every known Pokemon technique, the perfect specimen for cloning."

"But… why? What was the point of making Mewtwo?" Dawn asked.

"Partly to satisfy the one who had been funding my experiments at the time." Dr. Fuji answered. "He wanted to have the most powerful Pokemon in existence to use as a weapon. At the time it was a reasonable compromise, as no one else was willing to fund my experiments. Besides, I needed to create a Pokemon who was as strong as possible to survive my cloning techniques, all so that I could perfect them and make them usable for humans."

"You were planning to clone humans too?" a stunned Dawn asked.

"You remember when I told you that my daughter had died?" Dr. Fuji asked. "My work was an attempt to bring her back to life through cloning. At the time, I had almost succeeded in doing just that."

"But… even if you did manage to clone your daughter… that wouldn't really be bringing her back from the dead, would it?" Dawn asked.

"No… it probably wouldn't." Dr. Fuji admitted as he backed his chair away and turned towards the tube with the girl in it. "It's easy enough to clone living tissue, but it is probably impossible to clone the soul. I suppose I was chasing an illusion back then. In any case, when the first clone of Amber died, I devoted myself entirely to Mewtwo. Mewtwo survived the cloning process. He was my greatest achievement… and my greatest mistake. He lashed out at my colleagues and I, destroying our lab soon after he had awakened. That is why I have these scars all over my body and why I'm bound to this chair.

"I would probably have died that day had it not been for one of my benefactor's men finding me and taking me to the hospital. After I had recovered from my ordeal, I decided to move the Kalos Region and disappear, put everything that had happened behind me."

"Well if that's true, then what the hell is all this?" Dawn asked. "You said that you tried to put what happened behind you, but it looks like you've set up another lab and you have Mewtwo in this tube!"

"Yes… I was indeed unable to escape my past. But then I suppose that I never wanted to escape it to begin with." Dr. Fuji admitted. "To answer your question, Ms. Berlitz, that Mewtwo in the tank there is not the original one. It is the second member of its species."

"So… you cloned Mewtwo?" Dawn asked. "But how?"

"This Mewtwo was made from a fresh sample of Mew DNA." Dr. Fuji revealed. "My new benefactor was able to salvage much of my original research notes, and using them I was able to recreate my original experiment."

"New benefactor?" Dawn repeated. "I don't understand. Someone asked you to do all this again?"

"Let me start from the beginning." Dr. Fuji responded. "After I had recovered from my ordeal with the original Mewtwo and moved to the Kalos Region, I found that I was obsessed with trying to figure out what had gone wrong my original clone of Amber. Even after everything that happened, I wanted to try again. Then one day, a man came before me with a very unusual request. Tell me Ms. Berlitz, have you ever heard of something called Mega Evolution?"

"No. What is it?" Dawn asked.

"It's a fairly recent discovery, so I'm not surprised you have heard of it." Dr. Fuji replied. "Unlike normal Pokemon evolution, Mega Evolution is a temporary transformation that some Pokemon are able to undergo during a battle. This transformation heightens the Pokemon's abilities, making them even stronger than before."

"And… what causes this transformation you're talking about?" Dawn asked.

"A special kind of stone that's called a Mega Stone." Dr. Fuji answered. "There are different kinds of stones for specific Pokemon. In fact there are two different stones for the Pokemon, Charizard. Each stone triggers a different Mega Evolution. The man I mentioned before had analyzed various different Mega Stones and managed to create an artificial variety. But he found that there was no Pokemon that his artificial stone would work on though. The only Pokemon who's DNA even came close to being affected by the stone's energy was Mew. When he discovered this, he sought me out and asked me to create a second Mewtwo in order to see if the artificial stone would work on it."

"So you just happily said yes." Dawn realized. "And now you have another Mewtwo."

"I've been calling this one, Mewtwo Zwei." Dr. Fuji revealed. "It seemed a little more elegant than calling it Mewtwo Two. But the main reason I accepted my current benefactor's request was because it gave an opportunity to perfect my work. And now it seems that at last I have. Weren't you ever going to ever ask me about my other specimen?"

Dawn realized that Dr. Fuji was talking about the girl in the other tube. As she turned to look at the other tube, her eyes caught something at the container's base. It was a brass plaque with the word, Drei written on it. Dawn looked down at the base of the Mewtwo's tank and saw another plaque with the word, Zwei. Just then Dawn recalled something that Dr. Fuji had said earlier during their conversation. He had said that he focused totally on creating the original Mewtwo after his first clone of Amber had died. Dawn then remembered the picture of Amber and how she had long green hair just like the girl in the tank.

"That girl… she's a clone of your daughter?" Dawn realized.

"Very astute, Ms. Berlitz." Dr. Fuji confirmed. "The young woman you see before you here is a clone I made using the only fragment of Amber's DNA that I had left. I used what I had learned from my work with the original Mewtwo and figured out a way to successfully clone a human. Do you care to know what the secret is, Ms. Berlitz?"

"I'm… I'm not sure." Dawn answered.

Dr. Fuji merely chuckled. "Part of the reason behind Mewtwo's ability to survive the cloning process was his psychic powers. Taking that into account, I spliced the sample of Amber's DNA with genes from well-known humans with psychic abilities. She contains genes from Sabrina, the leader of the Saffron City Gym in the Kanto Region, as well as genes from Caitlin of the Unova Region's Elite Four. As a result, this clone of Amber possesses the same psychic powers that they do."

"But… that still isn't really your daughter!" Dawn told him. "This whole thing is just nuts!"

Dr. Fuji put his hand on the glass of Amber's tube. "She may not truly be my daughter, but she is the perfect human being."

Suddenly the glass tube containing Dr. Fuji's second Mewtwo began to crack. The sound caused Dawn, Dr. Fuji and Piplup to look and see that the feline Pokemon's eyes had opened and were glowing with a blue light. Suddenly the glass tube shattered and the yellow liquid inside spilled out like a wave. The newly awakened Mewtwo was now sitting on the bottom of what was once its tank.

"Wonderful!" Dr. Fuji declared with excitement. "Our conversation must have caused it to awaken. The time has now come for me to use the item I obtained for this very moment."

Dr. Fuji quickly reached into a bag hanging on the side of his wheelchair and produced a very unique-looking pokeball. The top half of it was purple and had two pink dots on the top, and right above the button on the front was a while letter M. Dawn recognized the pokeball as a Master Ball, the ultimate achievement in pokeball technology. Dr. Fuji threw the ball at Mewtwo before it could react, hitting the psychic feline in the forehead. Mewtwo was turned into a red energy and pulled inside the ball. The ball dropped to the bottom of the broken tank and jiggled for a few moments before making the signal that the capture was complete.

"There we are." Dr. Fuji spoke as he moved his wheelchair over and picked up the ball. "Hopefully this will help to keep history from repeating itself."

"Was that really necessary?" Dawn asked. "That Pokemon only just woke up, and you go and capture it with a pokeball?"

"It was a necessary step for me to take." Dr. Fuji told her. "This will not only keep Mewtwo from destroying the lab the way that the first one did, capturing it was all part of the next phase of the experiment."

Just then, all the pieces of electronic equipment in the room began to beep wildly. Dr. Fuji and Dawn looked and saw that many of the computer screens at the back of the lab were flashing some kind of alert message. At the same time, the glass tube containing Amber began to crack. The glass shattered, releasing another tidal wave of yellow liquid onto the floor. With the liquid gone, the young woman inside dropped to the bottom of her tank and was gasping for air.

"Ms. Berlitz! Quickly! Put that towel over there on her!" Dr. Fuji ordered.

Completely forgetting the strangeness of the entire situation, Dawn saw the large white towel sitting on the metal table that Dr. Fuji was pointing to behind her and grabbed it. She then quickly rushed over and put the towel over Amber as she finished catching her breath. When her breathing finally became regular, the green-haired girl sat up and removed the strange visor that had been covering her eyes.

Dr. Fuji wheeled his chair over and smiled at her. "Hello Amber. You don't know how long I've been waiting for this day."

"You… are my father?" Amber spoke.

"She… she can talk?" a stunned Dawn asked.

"The device you saw covering her eyes earlier has been sending information from the lab's main computer directly to her brain since she first started to develop, educating her." Dr. Fuji explained. "It not only taught her how to talk and read, it also gave her knowledge on a vast amount of topics, even giving her complete information on every Pokemon known to exist. I also gave her knowledge of my identity."

After a moment, Amber finally stood up and stepped off the remains of her tank, keeping the towel wrapped around her as she looked around the lab. "Where… is my friend? The one who I've been talking to for as long as I can remember?"

"Her friend?" Dawn repeated with a raised eyebrow.

"Ah, of course! Your friend is right here, Amber." Dr. Fuji told her as he handed her Mewtwo's pokeball. "I apologize for interrupting your long conversation, but I had to put your friend in this ball. Go ahead and throw it and your friend will emerge."

Amber looked at the ball for a moment before finally throwing it like Dr. Fuji told her. The ball opened up in midair and Mewtwo emerged with a burst of light.

The psychic feline looked around the room. "Where am I?"

"It's a girl?" Dawn realized after hearing the Pokemon's distinctly female voice inside her head.

"It would appear so." Dr. Fuji confirmed. "That was something I was not expecting. Either the original DNA sample was from a female Mew, or I tweaked a chromosome without realizing it."

Amber smiled and walked up to Mewtwo. "Hello there. This is the first time we're meeting like this."

"You're… Amber." Mewtwo realized. "The one who I've been conversing with."

"They already know each other?" a confused Dawn asked. "How is that possible?"

"As I suspected, Amber and this Mewtwo have been communicating telepathically this whole time." Dr. Fuji explained. "The same thing happened during my original experiment. Interrupting them by capturing this Mewtwo in a pokeball is likely what caused Amber to awaken."

"Mewtwo?" the Pokemon repeated. "Is that what I am?"

"That's your species, right father?" Amber replied.

"That's correct, Amber." Dr. Fuji confirmed. "You are the second Mewtwo that I created."

"So… I am not the only one of my kind." Mewtwo realized.

"Zwei." Amber spoke. "That's what I'll call you."

"Zwei?" Mewtwo repeated with a quirked brow.

"It's another word for the number two." Amber explained. "It's also the word on your tank. Since you're the second of your kind to exist, it seems appropriate. Plus… I think it's kind of pretty."

"I think it's an excellent nickname." Dr. Fuji agreed.

The psychic feline was silent for a moment. "That name seems acceptable."

"Well, now that all that's settled, I think we should all go to bed." Dr. Fuji decided. "Amber, I'll show you and Zwei to your room. The two of you are going to have a big day ahead of you tomorrow."

"What do you mean, father?" Amber asked.

"I'll explain in the morning." Dr. Fuji told her. "Ms. Berlitz, I think you should go to bed as well. You must be tired after all that's gone on."

"Uh, yeah. Piplup and I really should turn in." Dawn agreed. "It's nice to meet you Amber, Zwei."

Dawn and Piplup left the laboratory as calmly but quickly as possible. Within a few short minutes they were safely back in their room. Piplup had been so unsettled by the night's events that Dawn let him climb into bed with her. The little penguin Pokemon was out like a light in less than a minute, but Dawn was finding it especially hard to get to sleep. Her mind was reeling over everything she had just seen. Not only had she just encountered the second Mewtwo to ever exist, she had also met a young woman who Dr. Fuji had grown in a test tube and programed like a computer. It all seemed so unreal, and yet at the same time the whole thing was too real to deny.

After turning onto her side, Dawn looked at the pokeballs sitting on the dresser of her room. Her eyes settled on a pokeball with a sparkling pink top. That pokeball contained her secret weapon, the one Pokemon she had that could potentially stand against Zwei if things got bad. Taking comfort in the fact that she had an ace in the hole, Dawn finally drifted off into a dreamless sleep.

* * *

 **Author's Note:** One of the flaws with Mewtwo's ability to Mega Evolve in the games is, how could it be possible for there to be two different stones in nature that just happened to be able to induce Mega Evolution in an artificially created Pokemon? The only way I could see that happening is that if the Mega Stone for Mewtwo were also synthetically made. So one of my reasons for doing this story was to address that little issue.

Please review and let me know what you think.


	3. Phase 2

**Author's Note:** I was going to wait until tomorrow to post this chapter and the next one, but since I wanted to swing by the site to send a quick PM I thought I'd go ahead and put them up now. The truth is I've been working on the story since last Saturday.

 **Disclaimer:** I do not own Pokemon.

* * *

Chapter 3: Phase 2

Despite getting to sleep so late due to the strange events from the night before, Dawn had woken up fairly early that morning. It didn't help that all the bird Pokemon indigenous to that tropical island seemed to like to sing to each at around the crack of dawn. One of the loudest of these birds was a Chatot that Dawn saw perched outside one of her windows when she woke up that was spouting some of the more colorful four-letter words of the human language. Dawn had an already awake Piplup use is Bubble Beam attack to scare the offending bird off. With sleep no longer an option, Dawn had decided to go ahead and start the day, strange as she was sure it was going to be.

As soon as Dawn finished getting dressed, she started putting all six of her pokeballs onto her belt. The last ball she picked up was the one with the sparkling pink top, the one that contained the only Pokemon that could stand against Zwei if things got bad, Palkia. Dawn had obtained Palkia under a very bizarre set of circumstances. While investigating some old ruins on the Johto Region after learning her sister, Dusk had disappeared from there a month before, Dawn had encountered the mythical creator god Pokemon known as Arceus. For reasons that Dawn did not understand, Arceus had decided to gift Dawn with a newborn Palkia, the dragon from Sinnoh Region myth that was said to rule over space.

Dawn had learned years later that Arceus had also given her two sisters two of the other dragons of Sinnoh myth. Her sister Diane had been given a newborn Dialga, the dragon who was said to rule over time. Meanwhile, Dawn's sister Dusk had been given Giratina, the ghostly dragon who ruled the realm known as the Distortion World. Dawn still had no idea why Arceus had decided to give her and her sisters these dragons, but the one thing that Dawn did know at that moment was that Palkia was the only Pokemon she had that could match Zwei's level of power. Of course even with Palkia, Dawn wasn't sure if she could defeat Zwei in battle. During that day in Lavender Town when Dawn had her little reunion with her sisters, she had seen the original Mewtwo take down Diane's Dialga in battle. Granted, she and Palkia had already done some damage to Dialga and the original Mewtwo was more experience in battle than Zwei, but Dawn still feared that Palkia just might not be able to defeat Zwei should the worst happen.

The thought had also occurred to Dawn that she could just use Palkia to fly away from the island, but she found that she didn't want to leave. She was afraid that things with Amber and Zwei were going to get bad, and she wanted to be around in case they tried to harm Dr. Fuji or anyone else. As insane as Dawn thought the wheelchair bound scientist was; she just could leave him alone in case his newest creations lashed out at him. And Dawn knew that such a thing was a very real possibility. The original Mewtwo had lashed out at Dr. Fuji and destroyed his lab, even killing members of his staff in the process.

Dawn put Palkia's pokeball on her belt and headed for the dining room with Piplup. The blunette hoped that breakfast had at least been prepared. When Dawn arrived at the room with Piplup, she was a bit started to see Amber sitting at the table. The green-haired girl was wearing a white bodysuit that hugged tightly to her frame, along with a pair of black boots and a black belt with a square brass buckle.

Amber noticed Dawn's arrival almost immediately. "Oh! Hello there. You're the girl I saw in father's lab last night. I think father said that your name was Ms. Berlitz?"

"Uh, yeah. But you can just call me Dawn." The blunette replied as she sat at the table. "Where's Zwei? Is she in her ball?"

"She's outside." Amber answered. "Everything about this world is no new to her, and she couldn't help but go outside to take a look around. So father said that you're a Pokemon Coordinator?"

"That's right. I was actually on my way to a contest in the Kalos Region before I ended up here." Dawn explained. "So… how do you like this place so far?"

"Well, I like the house where my father and I lived before, but this place isn't so bad." Amber answered.

Amber's comment raised a red flag in Dawn's mind. Up until the previous night, Amber hadn't been outside the tube of liquid that Dr. Fuji had grown her in. How could she remember living in a house with her father?

"So Dawn, what's your father like?" Amber suddenly asked.

"Um, I don't really remember, to be honest." Dawn answered. "He died when I was very young. I do have a mom and two sisters though. My mom was a Pokemon Coordinator too."

"And are your sisters also coordinators?" Amber asked.

"No. My sister Diane is a Pokemon researcher." Dawn answered. "And Dusk, well… let's just say that she's a different kind of trainer."

"Are you and your sisters close?" Amber asked.

"Actually we've always had a little trouble getting along." Dawn admitted. "In fact the last time we met we got into a pretty big fight. We managed to patch a lot of things up though."

"I kind of wish I had sisters of my own." Amber replied. "I guess the only person who even comes close to that is Zwei."

"Amber?" a voice suddenly spoke. Dawn and Amber looked to see Dr. Fuji in the doorway. "If you're finished eating, please fetch Zwei and come to my lab. We have a lot of work to do today."

"Yes father." Amber responded before getting up and leaving the room.

As soon as Amber was gone, Dawn got up to talk to her creator. "Dr. Fuji. Amber told me something that was kind of odd. She said that she remembers living with you in another house, but how is that possible? I mean… before last night she was… in your lab."

"Yes, well… I suppose I should explain that in order to avoid certain… complications." Dr. Fuji began. "Part of Amber's 'education' included details about my daughter's life. Specifically old family videos of her that I've always kept."

"But… Amber seems to think that she really is your daughter, I mean the original Amber." Dawn told him.

"And for the time being, that is an illusion that I would like to maintain." Dr. Fuji requested. "I ask you, Ms. Berlitz, to keep the knowledge of what Amber truly is to yourself. It will be much easier on all of us if Amber believes she is the original for the time being. Now if you'll excuse me, I need to prepare the second phase of my experiment."

With that, Dr. Fuji rolled away to his lab. Dawn was left completely unsure about what to do. It didn't seem right to lie to Amber about who or rather what she really was. Then again, it also seemed cruel to simply shatter what Amber believed to be the truth. Plus there was the question of what Dr. Fuji might do to her if she went against his wishes.

* * *

Amber was sitting in a metal chair in Dr. Fuji's lab as he put a metal choker around her neck. It was made of a dark-grey metal and had a blue stone like a marble with a black mark in the middle fitted into the front. Zwei was standing across the room from Amber on a platform as Dr. Fuji fastened the choker onto her neck.

"What is this, father?" Amber asked as she touched her new piece of jewelry.

"That, daughter, is a special ring I had designed just for you." Dr. Fuji answered. "It contains a keystone, an object that is vital to my current research. And now, Zwei, it is time to fit you with your special jewelry."

"I am to be adorned as well?" Zwei asked with a quirked brow.

"Yes. Now if you will just hold still for a few moments." Dr. Fuji requested as he rolled is chair over to a set of controls in the lab. "This will not take long."

Dr. Fuji flipped a few switches and a pair of dark-grey mechanical arms came down from the ceiling. The metal pincers of the arms held a silver object that looked like a championship belt. The arms fastened the belt around Zwei's midsection. Fitted into the rectangular front piece of the belt was a large round pinkish stone.

"What is this?" Zwei asked.

"That band contains a special Mega Stone that was synthetically made." Dr. Fuji explained. "The person currently funding my research wants to know if this stone will cause you to Mega Evolve."

"I'm familiar with this Mega Evolution concept, but I didn't know it was possible to make artificial Mega Stones." Amber spoke. "Do you really think that stone will allow Zwei to Mega Evolve, father?"

"That's what we're going to find out." Dr. Fuji answered. "We're going to test this stone in battle."

"Amber and I are going to have a Pokemon battle?" Zwei asked. "Who will we be fighting?"

"My assistant, Muldoon." Dr. Fuji replied. "Among other things, he's a fairly skilled Pokemon trainer. He should be able to provide both of you with a decent challenge."

"Dr. Fuji… did you run any experiments like this with the original Mewtwo?" Zwei asked.

At this, Dr. Fuji paused. "Actually no. The first Mewtwo was a little more… independent. He left before any of my planned experiments could begin, and there was nothing I could do to stop him. Now, are the two of your ready to begin?"

"I am ready if Amber is." Zwei answered.

Amber looked at Zwei and nodded. "We're ready, father."

* * *

Dawn had decided to go out for a walk with Piplup to take a look around the island. There was nothing but tropical forest for miles around. The forest was filled with some fairly exotic Pokemon though. Dawn would've tried capturing a few of them if she had any spare pokeballs on her. As it was, she only had her old pokedex and the six Pokemon she had brought with her. Eventually Dawn and Piplup had found their way to the back the house. The area behind Dr. Fuji's mansion was a small clearing with white lines painted on the dirt. Dawn realized that the clearing had been set up as a field for Pokemon battles.

Next to the battlefield was a small wooden shed, and only seconds after Dawn and Piplup arrived the door the shed suddenly opened up. Walking out was a man who stood at about seven feet tall and appeared to be in his early forties. He was well muscled and had a thick brown beard. His outfit consisted of a short-sleeved olive green shirt with matching cargo shorts, along with black boots and a brown wide-brimmed hat that covered the top of his head. Hanging from the man's belt was a machete and four pokeballs, and around his right wrist was a thick black metal band with a round blue stone resembling a marble fitted into it.

Upon emerging from the little hut, the man noticed Dawn in an instant. "Well, well, well. Looks like sleepin' beauty finally woke up from 'er nap."

"Uh, hi. You must be Dr. Fuji's assistant, Muldoon." Dawn deduced. "Thank you for rescuing me before."

"Ah. T'weren't nothin' missy." Muldoon replied with a wave of his hand. "It's not like me to ignore a lady in distress. So, I take it yew been out exploring the island."

"Yeah. It's quite lovely." Dawn admitted.

"If ye want to so some Pokemon catchin' later, I can show yew some of the best huntin' spots on the island." Muldoon offered. "I also got some spare pokeballs yew can 'ave."

"Thanks. I may take you up on that later." Dawn replied. "It's not like there's much else for me to do here."

"Yeah… Pokemon hunting's the only good thing about this island." Muldoon told her. "It's certainly better than hangin' around my weird employer."

"So… you know about Dr. Fuji's work?" Dawn asked.

Muldoon looked her in the eye. "You've seen 'em, haven't ya missy? That girl and the Pokemon the ol' doc had growin' in those tubes? I 'ear they're up an' about now."

"Yeah. I've met them." Dawn admitted. "Amber at least seems nice. Have you met them yet?"

"No. But I'm about to." Muldoon answered. "The doc wants me to put 'em through their paces in a battle. Quite frankly, I don't know what ol' Dr. Fuji is up to, and I'd rather not ask too many questions 'bout it. All I care is that he's payin' me good money to look after his house, cook 'is meals, and test 'is little lab rats in battle."

"Ah! Ms. Berlitz. I've see you've met Muldoon." A familiar voice spoke. Dawn and Muldoon saw Dr. Fuji approaching with Amber and Zwei. "Well Muldoon? Are you ready?"

"As I'll ever be, doc." Muldoon answered as he took his place on the battlefield. "Let's get this started."

Amber took her place at the other end of the battlefield. "Let's go, Zwei."

Zwei nodded and flew out onto the battlefield. Dawn and Piplup went over to stand next to Dr. Fuji. From their new position, Dawn saw that Dr. Fuji had set up a video camera to record the battle.

Muldoon threw out a pokeball. "Go Rhyperior!"

Bursting out of Muldoon's thrown ball was an enormous creature that resembled a cross between a rhino and a dinosaur. It stood at about seven feet tall and was mostly dirt-brown in color. Red stone plates covered its chest and the back of its head like armor. On its nose was a silver drill-like horn, and there was a small silver horn on its forehead. Its tail resembled a club, and it had large forearms with long flat spikes on its elbows. The creature's hands had three thick white fingers with flat tips, and in each palm was a large hole.

"Use Bulldoze!" Muldoon ordered.

"Dodge and use Confusion!" Amber commanded.

Rhyperior roared and stomped the grounded with his right foot, sending a wave of spikes shooting up from the ground towards Zwei. The psychic feline flew up into the air before the front of the attack could strike her. Zwei's purple eyes began to glow blow, and at the same time, Rhyperior began to give off a feint blue aura. With a wave of Zwei's hand, the rhino creature was lifted off the air and hurled into a large tree next to the battlefield, breaking it in half. After a few moments, Rhyperior got back up and lumbered back onto the field, glaring up at Zwei as he did so.

"Ye'r not gonna beat us that easily, beastie!" Muldoon declared. "Rhyperior! Use Rock Wrecker!"

"Use Confusion once more!" Amber ordered.

Rhyperior brought his hands close together and small pebbles began to shoot out of the holes in his palms, mashing together to become a single floating boulder that glowed with a red aura. The rock Pokemon fired the stone projectile up into the air towards Zwei. Just before the boulder could strike though, Zwei's eyes glowed and the rock froze in midair. A split second later, the boulder shattered apart. Zwei raised her hand forward, and Rhyperior glowed with a blue aura and was slammed down to the ground hard. When the attack ended, Rhyperior was out cold.

Muldoon scowled as he called Rhyperior back to his ball. At the same time, Zwei floated back down to the ground.

Zwei's lips curved into a smirk. "That was too easy."

"Muldoon! I believe it's time to take things to the next level." Dr. Fuji decided.

"You got it, doc!" Muldoon replied as he took out another pokeball. "Go Aggron!"

Bursting from the thrown ball was a large dark-grey creature resembling a dinosaur or lizard. It stood on its hind legs and had a very well developed tail. Silvery armored plates almost resembling a mask covered its face. Growing through two holes on the plate covering its forehead were two long straight silver horns. Bands of silver armor also covered the Pokemon's legs. Four thick black leather straps covered Aggron's torso, joined together on the chest by a round greyish stone.

"Watch closely, Ms. Berlitz." Dr. Fuji told her. "You're about to see the power of Mega Evolution in action."

"Now ye'r in for it, ya test tube beastie!" Muldoon declared as he raised his right wrist. "Use Iron Head!"

The stone embedded in the ring on Muldoon's wrist began to shine with a bright light. At the same time, Aggron roared and the stone mounted on his chest began to glow as well. Suddenly the armored creature roared and glowed with a grey light. When the light faded, Aggron had taken on a new form. He had grown much larger and the bumps on his round shoulders had turned into blade-like spikes. Thick pieces of silver armor were covering his chest, waist and legs. There were also thick bands of silver armor with narrow spikes on them covering the creature's forearms. The mask-like armor covering Aggron's head had become thicker, and he had gained a set of serrated jaws and a single blade-like spike on the top of his snout. A multicolored light in the form of a DNA strand glowed briefly above Aggron's head before suddenly vanishing.

Aggron's sudden transformation caused Amber to gasp and Zwei to quirk her brow. The steel behemoth began to charge towards Zwei as the armor covering his head began to glow white, the ground shaking each time he took a step. Aggron rammed into Zwei at full force, knocking the psychic feline into a tree behind Amber. Zwei quickly recovered from the attack and flew back onto the field.

"Use Confusion again!" Amber commanded.

Zwei's eyes glowed again, and with a wave of her hand Aggron glowed with a blue aura and was thrown into the same spot that Rhyperior was thrown into earlier. It wasn't very long before Aggron got back up. The armored titan glared at Zwei as he lumbered slowly back onto the field, each step he made causing a small tremor in the ground.

"Is Confusion the only attack Zwei knows?" Dawn asked.

"The only one that's even remotely effective." Dr. Fuji answered. "Zwei is technically a newborn, after all. It will take her time to learn more powerful moves."

"And you're having Amber and Zwei battle such a strong opponent so soon?" a surprised Dawn asked. "I don't know anything about this whole Mega Evolution thing, but I can tell that Mr. Muldoon's Aggron is a really well-trained Pokemon!"

"Indeed." Dr. Fuji agreed. "But if the synthetic Mega Stone equipped to Zwei works, it should turn the tide of this battle in an instant."

"Use Heavy Slam!" Muldoon ordered.

Aggron roared and charged full speed at Zwei as he began to glow with a white aura. Before Zwei could get out of the way, the armored behemoth tackled her hard to the ground with enough force to make a small crater.

"Now follow it up with Iron Tail!" Muldoon commanded.

Aggron got off of Zwei, and before the psychic feline could fully get up her opponent struck her with a glowing white tail, flinging her back into another tree behind Amber.

After a few moments, Zwei got back up. "I… will not… lose to you!"

"Zwei! Use… use Focus Blast!" Amber commanded.

Zwei brought her hands together and a ball of blue light formed between them. When the ball got large enough, the feline fired it at Aggron and hit him in his armored chest. The impact from the blast had caused Aggron to be pushed back at least half a foot.

"Not bad, girlie!" Muldoon praised. "That attack actually did a li'l damage! Unfortunately for you, my Aggron has an ability called Filter when he's Mega Evolved like this. Filter lowers the damage from super effective moves like Focus Blast. It'll take a li'l more than what you've got to beat us."

"Zwei! Use Focus Blast again!" Amber ordered.

Zwei fired another ball of blue light at Aggron, this time hitting him in the stomach. Once again the armored Pokemon was pushed back another half a foot.

"Focus Blast one more time!" Amber commanded.

Zwei charged up another ball of light that was twice as large as the first two. The psychic feline launched it at Aggron, striking him in the chest again. This time, Aggron had almost been knocked onto his side.

"Finish it with Confusion!" Amber commanded.

Zwei's eyes glowed blue again, and with a movement from her hand Aggron was lifted off the ground and several feet into the air. With a wave of her arm, Aggron was slammed back hard into the ground, creating a crater that was at least five feet deep. Aggron suddenly reverted back into his original form and was out cold. At the same time, Zwei fell to one knee but was still conscious.

"You did well, Zwei." Amber told her. "Rest for now."

With that, Amber called Zwei back to her pokeball. Muldoon grumbled to himself as he called back Aggron as well.

"Well… the results of this first battle were certainly disappointing." Dr. Fuji remarked as he stroked his beard. "I had hoped that the close bond that Amber and Zwei developed during their conception would have caused their Keystone and Mega Stone to react. But I suppose that it will take time to truly see whether or not the artificial stone is truly effective."

"Hey doc! If ye'r done with me for now, I got some other work that needs doin'!" Muldoon informed him.

"Yes, yes. Carry on, Muldoon." Dr. Fuji replied with a wave of his hand. Muldoon walked off and focused his attention on Amber. "Now then, Amber. If you'll come with me, I need your help in the lab with another experiment."

"Do you need Zwei's help as well?" Amber asked.

"No. This is something that only you can help me with." Dr. Fuji answered. "Ms. Berlitz, if you'll excuse us."

Dawn and Piplup watched as Dr. Fuji left with Amber. After a few moments, Dawn finally decided to head back into the house.

"I have a bad feeling about all of this, Piplup." Dawn told her penguin companion. "I don't know what Dr. Fuji has planned for Amber, but I don't think it'll end well."

* * *

 **Author's Note:** I hope nobody thought it was weird to see Zwei almost seem to lose the battle in this chapter. She may be a Mewtwo, but that was her first time in battle. Plus bare in mind that when the original Mewtwo destroyed Dr. Fuji's lab in the anime, he was only attacking a bunch of defenseless scientists. The next chapter is already up, so go ahead and take a look.

Also if you want, please review and let me know what you think.


	4. The Room of Pain

**Disclaimer:** I do not own Pokemon.

* * *

Chapter 4: The Room of Pain

It was a cloudy day as Dawn and Piplup followed Muldoon into the island's tropical forest. Dawn had decided to take Muldoon on his offer to look for new Pokemon from two days earlier before he battled Amber and Zwei. Going on a little expedition into the woods was certainly better than just sitting around the house waiting for something to happen, and Dawn felt like it was only a matter of time before it did. It seemed like she was sitting on a time bomb, waiting for Dr. Fuji's little experiment to somehow go awry. And there was really nothing that Dawn could think of to do about it, short of having Palkia tear the house apart, but Dawn felt that was a little extreme.

There was a rumble of thunder as though it was going to rain soon as Muldoon hacked apart a vine with his machete. He stopped and motioned Dawn to come closer with a wave of his hand. Dawn silently approached and saw a Pokemon before them in the clearing. It was a tiny mouse-like creature that was mostly yellow orange in color. It had round black ears that were cream colored on the inside and a black tail with a spiked tuft of fur at the end. Its stomach was the same color as its ears, and it had two round orange circles covering its cheeks. Growing from these circles were two pairs of black whiskers that resembled T.V. antenna. The little rodent was sitting in the clearing eating a berry, totally oblivious to Dawn and Muldoon watching it.

Dawn couldn't help but squeal upon seeing the little mouse. "Oh my god! That is one of the cutest Pokemon ever!"

Piplup let out a small cry and puffed out his cheeks. Dawn could tell that the little penguin seemed offended by her comment.

Dawn crouched down and patted Piplup on the head. "Aw. Don't be like that, Piplup. You're just as cute as ever."

"That li'l fella there is called a Dedenne." Muldoon informed her. "It's an Electric and Fairy-type Pokemon. If ya wanna catch it, now'd be the right time."

"Okay Piplup. Use a Bubble Beam on Dedenne there." Dawn politely requested.

After a moment, Piplup got over his hurt feelings and fired a barrage of bubbles from his beak. Dedenne was struck in the side by the attack and fell onto its stomach. Dawn took the opportunity and threw one of the empty pokeballs that Muldoon had given her. The ball struck the electric mouse on its back and sucked it inside. The ball jiggled for a few moments before making a signal that the capture had been completed. A second later, the ball flashed white and vanished.

"That was an easy capture." Dawn remarked.

Just then another Pokemon suddenly wandered into the little clearing. The creature was a fairly small slug-like blob that was light purple on top and dark purple on the bottom. It had two beady black eyes and five large green dots on the sides of its body. On the top of what could be considered its head two four horn-like feelers, with the two in front being longer than the two at the back.

"Well, well. We're certainly gettin' a lot of luck on this li'l hunt." Muldoon whispered. "That there, missy is called a Goomy, a pretty rare Dragon-type Pokemon. The weather we got right now musta brought this one outta hidin'."

"Okay Piplup. Use Ice Beam on that Goomy." Dawn quietly ordered.

Piplup nodded and fired bolts of white electricity into the clearing, striking Goomy as it slowly slithered its way across. The dragon slug was hit in the side by the attack and frozen in a block of ice. Dawn threw another empty pokeball at Goomy. Goomy was pulled inside, and the ball only jiggled on the ground for a few moments before making the sound that signaled a completed capture. Soon after, the ball vanished with a flash of white light.

"Guess I'm two for two." Dawn observed. "I'm a little surprised that Goomy was such an easy catch though, since it's a dragon."

"Goomy are known for bein' the weakest Dragon Pokemon out there." Muldoon explained. "We're not too far from the beach. What say we take a break out there for a bite?"

"Sounds good." Dawn agreed.

With that, Dawn and Piplup followed Muldoon as he led the out of the forest to the section of beach on the outer rim of the island. When they exited the forest, they found a pair of large rocks on the beach and sat down on them to have their lunch, which they had brought with in three small bags that Muldoon had prepared earlier, one of which contained food for Piplup. They ate largely in silence. When Dawn had finished her meal, she pulled out her pink pokedex and began pressing a few buttons.

"Let's see… I think I'll send Togekiss and Pachirisu back to Professor Rowan's lab and send Dedenne and Goomy here." Dawn decided.

With the press of one final button, two of the pokeballs strapped to Dawn's belt glowed white and changed into the balls she had earlier used to capture Goomy and Dedenne. Dawn threw the two balls out and her two new Pokemon emerged.

"Hi there." Dawn greeted. "Sorry I was so rough on you two earlier. I'm Dawn, and this is Piplup."

After a moment, Dedenne scurried up to Dawn and crawled up her leg and onto her shoulder. Dawn smiled and patted the tiny electric mouse on the head. Piplup meanwhile went over and introduced himself to Goomy. The dragon slug brushed into Piplup in a friendly manner, causing a string of slimy mucus to form between them. Piplup let out a small cry of disgust.

"Ya don't often see trainers use the Pokemon transfer system built into their pokedex." Muldoon remarked. "Most of 'em just use the PCs in the Pokemon Centers."

"Yeah, well it's not like I have a lot of other options on this island." Dawn pointed out. "I'm pretty much cut off from the rest of the world until that supply ship gets here, and that's not going to be for a few weeks."

"Well, at least ya got a couple of new friends to enjoy yer say with." Muldoon pointed out as he pulled a flask out of his pack.

"True." Dawn replied. "So Mr. Muldoon, how long have you been working for Dr. Fuji?"

"Ever since 'e set up shop on this li'l island and began those daft experiments of 'is." Muldoon answered after taking a swig from his flask. "Before that, I was a deputy warden at the Kanto Safari Zone."

"Why'd you leave that job?" Dawn asked.

"Well missy… let's just say I was relieved of my duties because I overindulged a bit during an afternoon shift." Muldoon answered, shaking his flask a bit to explain what he meant. "And 'cause of that, a heard of Rhyhorn got loose an' almost ran over the chief warden's grandkid. I was sacked right 'ere on the spot."

"I'm… I'm sorry to hear that." Dawn told him, though she wasn't entirely truthful.

Muldoon waved his hand and took another swig from his flask. "T'was my own bloody fault. Besides, this job ain't all that bad. Pays better than my job at the Safari Zone. Wasn't quite what I was expectin' when I signed on though. Certainly never thought I'd 'ave to do any bloomin' housework, but then the ol' doc can only do so much with those gimp legs of 'is."

"Well, you certainly weren't what I expected you'd be when Dr. Fuji described you." Dawn admitted.

"An' just how did ol' Doc Fuji describe me?" Muldoon asked.

"Well… he called you his manservant." Dawn answered somewhat reluctantly.

Muldoon let out a deep hearty laugh. "Yeah? Well let the 'im think what he wants! He's completely bugger anyway!"

"Did… did you know that Dr. Fuji made another Pokemon like the one you battled before years ago?" Dawn asked.

Muldoon's expression became serious and he took yet another swig from his flask. "Yeah, 'e mentioned it to me once… when this whole thing started. The ol' doc's completely out a 'is mind, 'e is. An' what really makes 'im daft is that 'e don't see that girl 'e grew in that lab as a human bein'. To 'im, she's just some thing that 'e can toy with."

"What do you think about Amber? Do you think she's human?" Dawn asked.

"…Damed if I know." Muldoon answered. "She certainly didn't come into this world as a proper human ought to. What do you think, missy? Do you think she's a proper human bein'?"

"I think she is." Dawn answered. "But you're right… I don't think that Dr. Fuji sees Amber that way. And I'm pretty sure that something bad will happen because of it."

"To 'er or to us?" Muldoon asked.

"I don't know… maybe both." Dawn answered. "I just have a bad feeling about everything that's going on. The last time I bumped into Amber, she seemed so cold and distant. I think Dr. Fuji might be doing something bad to her."

"Yeah, well… there's not much we can do about it, missy." Muldoon told her as he got up. "Just sit back and wait things out 'til that ship get 'ere, that's my advice. As for me, I got me own coapin' mechanism right 'ere." The former safari warden shook his flask again to show what he was talking about. "Now, I think we should get back to the house before it starts to rain."

With that, Dawn called Goomy back to its ball and followed after Muldoon back to the forest with Piplup following close behind. She let Dedenne ride on her shoulder for the trip back. Dawn didn't entirely trust Muldoon, but she found that she felt better talking to someone besides Piplup about everything that was happening on the island. Of course she still didn't have a solution to the problem with Dr. Fuji, and it didn't seem like Muldoon was going to be much assistance. At that moment, Dawn was reluctant to do anything except wait and pray for the best.

* * *

As the rain started to come down outside, Zwei flew in through the large window of Amber's upstairs bedroom. The psychic feline had taken to exploring the island in the mornings out of sheer curiosity. Zwei found Amber still in her bed, lying in a fetal position. For the past two days, Zwei had been troubled by Amber's behavior ever since she started the solo experiments with Dr. Fuji. What was most troubling was that Amber had closed off her mind to her for some reason. Zwei decided at that moment that enough was enough. She needed to know what was wrong with her friend.

"Amber?" Zwei spoke. "Are you okay?"

"I'm fine, Zwei. Just tired." Amber told her. "Father's last experiment went late last night, that's all."

"I do not believe you." Zwei told her. "I can tell that you've been in pain. Why won't you tell me what's wrong?"

"I told you! I'm fine!" Amber insisted. "Now leave me alone!"

Zwei reached over and put a hand on her shoulder. "Amber, I'm very worried about you! Why won't you tell me what's wrong? Please… open your mind to me."

Amber sat up a little in her bed and nodded. Zwei peered into her green-haired trainer's mind. Suddenly the feline was assaulted by images of Amber strapped into some kind of chair with some kind of device on her head. She also felt the sensation of hot needles burrowing deep into her skull, the very pain that Amber was feeling in the visions. Zwei could also hear Amber's voice begging for her father to stop, but in the visions Dr. Fuji merely looked at the screen of a computer in the lab with a cold indifferent expression on his face.

Zwei quickly cut her mental link with Amber and cried out in anger. The large mirror on the dresser in Amber's room was suddenly shattered by an invisible force.

"How could he?" Zwei spoke with anger filling her voice. "I will tear Dr. Fuji to pieces!"

"No don't!" Amber begged as she grabbed hold of Zwei's arm. "Please Zwei! Don't hurt him."

"But Amber! He's hurting you!" Zwei pointed out.

"I know, but… he's still my father!" Amber told her with tears in her eyes. "That's why… that's why I shut myself off to you. I knew that if you found out what father was doing, you'd want to hurt him. And I… I don't want that to happen."

"Amber…" Zwei spoke, her expression softening.

Amber managed to compose herself a little. "I don't know what the purpose of father's experiments on is, but I'm sure there's a good reason behind them. So even though it hurts, I'm going to continue to help him with his work."

"…Very well." Zwei agreed after a moment. "I won't do anything to harm Dr. Fuji… at least for now. But if your life is in danger, I will act. You are my closest and only friend, Amber. I don't think I could take it if you were to die."

"Thank you for understanding, Zwei." Amber replied as she lied back down. "Now could you close the curtains? The light hurts my eyes right now."

Zwei turned to look at the curtains and her eyes began to glow, causing the curtains of the large window to shut on their own. Amber closed her eyes and drifted off to sleep. Zwei remained standing where she was and watched her trainer intently. She wanted to make sure that nothing happened to her while she was asleep.

* * *

It was the dead of night as Dawn shot up in her bed. She had just had a nightmare where Amber had Zwei pull Dr. Fuji's head off with her psychic powers and ordered the feline to do the same to her. Dawn realized that life on Dr. Fuji's island was starting to get to her. As she got out of bed, Dawn saw Piplup sleeping on his back in a corner of the room with Dedenne sleeping across his stomach. Despite Piplup getting upset about Dawn's comment about Dedenne earlier that morning before capturing him, the two Pokemon had ended up becoming friends very quickly. The sight of the two sleeping in a pile like that brought a smile to Dawn's face. Dawn decided that Piplup and Dedenne were too cute to wake up and got out of bed as quietly as she could.

After grabbing one of her pokeballs from the dresser, Dawn left the room and headed for Dr. Fuji's library. Even though she knew that the library was also the secret entrance to her host's lab, Dawn decided to try reading a dull book again to get back to sleep. It seemed impossible to get back to sleep any other way, not after the nightmare she had just experienced. When she got to the library, Dawn saw that the entrance to Dr. Fuji's lab had been left open. The blunette assumed that the scientist was so busy conducting another experiment that he forgot to close the door.

Dawn attempted to ignore the open lab and began searching the shelves for a book. Her search was interrupted though when she heard a scream come from inside the lab. She recognized that the scream was in Amber's voice. Dawn took a firm hold of the pokeball she had taken with her and dashed into the lab. Inside, she saw light coming from a smaller door in the corner of the lab that was open a crack. Without hesitating, Dawn burst through the door and was instantly shocked by what she saw in the room.

Amber was strapped into a reclined metal chair and had on some kind of strange metal helmet with thick cables leading back into the wall behind her. The helmet was giving off some sort of electrical discharges, and from the angle that Amber was leaning back, Dawn could see red laser beams inside the helmet that were firing into Amber's forehead. Whatever was happening seemed to be causing Amber great pain. As all this was going on, Dr. Fuji was at a computer station at a back corner of the room looking at a screen with a furrowed brow.

"I don't know what the hell is going on, but this has gone on long enough!" Dawn declared as she threw her pokeball. "Typhlosion! Spotlight!"

Bursting out of Dawn's thrown ball was a large creature that looked like a cross between a bear and badger. It was mostly dark-blue in color and had a cream-colored chest and stomach. Round red vents were around the back of the Pokemon's neck, and when it roared spiked flames erupted from those vents.

Dawn scanned the back of the room and saw what looked like some kind of fuse box mounted on the wall. "Typhlosion! Hit that box over there with Flamethrower!"

Typhlosion opened his mouth and breathed out a stream of red flames across the room and hit the box. As soon as the metal box was hit, it gave off sparks and the lights inside the room flickered. Soon after, the device that was on Amber's head stopped functioning.

Dr. Fuji scowled and wheeled away from the computer station. "Ms. Berlitz! While I appreciate your curiosity, this kind of interference is not something I tolerate!"

"What the hell were you doing to Amber?" Dawn demanded to know. "It looked like you were torturing her!"

"I was merely trying to stimulate Amber's psychic abilities!" Dr. Fuji explained as he went over and started undoing Amber's straps. "I will admit that the process is uncomfortable, but it is necessary if my work is to succeed! Now because of your heroics, my work will be set back for days, maybe longer! It all depends on how badly the damage you just did to my lab."

"Did you really expect me to just stand by and ignore you as you tortured Amber?" Dawn asked. "This… this whole thing is just twisted!"

"I don't expect someone like you to appreciate my work, Ms. Berlitz." Dr. Fuji told her. "I only expect you to not interfere."

"Like hell I won't!" Dawn shot back.

At that moment, Amber removed the helmet she had on and sat forward. "Dawn, please! Just do as my father asks. I know these experiments are painful, but I'm willing to endure them for his sake!"

"Amber… I don't think you realize who your father really is." Dawn told her. "Who you really are. And while I'm here, I can't let this thing go on! Now come with me! I'm getting you out of here!"

"I'm not going with you!" Amber told her.

"Amber…" Dawn began.

"I SAID NO!" Amber shouted. As she did, her eyes started to glow blue.

Suddenly Dawn was lifted off the ground by an invisible force and hurled into the wall behind her. Typhlosion roared at Amber, but the green-haired girl simply glared at the fire badger and hurled him against the wall he was standing in front of with the same psychic force, knocking him out cold. Amber's eyes stopped glowing and she let out a surprised gasp at what she had just done.

A triumphant smirk formed on Dr. Fuji's face. "Well Ms. Berlitz… it seems that I owe you a bit of an apology. Your interference tonight was just the stimulus Amber needed to trigger her psychic powers. Now, if you will excuse us… I have some notes to make. Amber, you can return to bed and we can begin the next phase of our experiments tomorrow."

Frightened, Dawn called Typhlosion back to his ball and ran from the lab as fast as she could. She didn't stop running until she reached the hallway where her room was. When Dawn went into her room, she saw that Piplup and Dedenne were still fast asleep as she set Typhlosion's pokeball back on the dresser. She then got back into bed and merely stared up at the ceiling. Dawn was at a total loss as to what to do. She knew that Dr. Fuji claimed that Amber had psychic powers of her own, but she never imagined that the green-haired clone could do anything that extreme. Her mind wandered back to her conversation with Muldoon before and how she said she thought that Amber was human despite how she was created in a lab. But after what had just happened, Dawn was no longer sure about that.

The only thing that Dawn was sure of was that what happened was probably going to give her a whole new set of nightmares.

* * *

 **Author's Note:** Sorry if the scene with Dawn and Muldoon at the beginning of this chapter seemed out of place. It seemed like a good way to flesh out Muldoon's character a bit, plus it was a good way to put some new Pokemon on Dawn's team that I could bring back in future stories. I can probably get some pretty amusing scenes out of the tendency of Goomy's fully evolved form to hug its trainer and cover them in slime. Imagine that happening to someone like Dawn.

Please review and let me know what you think.


	5. Research Notes

**Disclaimer:** I do not own Pokemon.

* * *

Chapter 5: Research Notes

The weeks that followed on Dr. Fuji's island had gone by slowly for Dawn. She did her best to avoid Dr. Fuji, Amber and Zwei as much as she could after that night in the lab when Amber demonstrated her powers. Dawn spent some of her afternoons on the island going on more hunting expeditions with Muldoon, though the former gamekeeper wasn't the most pleasant of company. In fact, Dawn was fairly certain that the Chatot that kept landing outside her window in the mornings to wake her up had learned much of its profanity from Muldoon. Much of Dawn's time on the island though was spent with her Pokemon perfecting new routines for future contests.

As all this was going on, Dr. Fuji's little experiment with Amber and Zwei was continuing. Dawn had no idea what had been going on in her host's lab since the night she interfered with his attempt to bring out Amber's psychic abilities, she didn't want to know. What Dawn did know though was that Amber and Zwei had continued to take on Muldoon in more Pokemon battles on a regular basis. Dawn had seen a few of those battles and could tell that Zwei was getting much stronger. Zwei had yet to Mega Evolve like Dr. Fuji wanted, which was probably a good thing, but it was quickly becoming effortless for Mewtwo to defeat Muldoon's Pokemon. Dawn had also noticed a change in Amber as well. The green-haired clone was becoming much colder and more ruthless in battle.

It was the morning of the day before the supply ship was due to arrive at the island, and Dawn was out behind the house wrapping up a new routine with Dedenne and Typhlosion. At almost the same moment as Dawn called Typhlosion back to his pokeball, Muldoon emerged from his shack.

"Ya might wanna make yerself scarce, missy." Muldoon suggested upon noticing Dawn. "The doc and 'is li'l science project are comin' back 'ere for another battle."

"Come now, Muldoon." Dr. Fuji spoke as he emerged from the house with Amber. "There's no need for Ms. Berlitz to leave just because she and I have had a few… disagreements. She's more than welcome to watch this next test of Amber and Zwei's power."

After a moment, Dawn decided to stay and watch Amber's battle. Dawn took a spot by the house with Piplup and Dedenne where they could avoid getting caught in the crossfire of the battle and at the same time stay as far away from Dr. Fuji as possible. As Amber took her position on the battlefield, she momentarily gave Dawn a cold stare.

"Right then. Let's get this started." Muldoon decided as he pulled out a pokeball. "Go Krookodile!"

Bursting out of the thrown ball was a large red crocodile-like creature with black stripes and a white underside. It stood on its hind legs and had well developed arms. Around its eyes was a black mask-like shape that gave one the impression that it was wearing sunglasses.

"Go Zwei!" Amber called as she threw her own pokeball.

The psychic feline burst from her ball and looked at Muldoon and Krookodile with indifference. "These opponents are starting to bore me."

"Me as well." Amber admitted. "Father, don't you have anyone stronger than this oaf?"

"I'm sorry, Amber. But Muldoon is the only available opponent for you right now." Dr. Fuji told her. "Until I can make other arrangements, you'll both just have to make due."

"You and that beastie a yours may 'ave beaten' me a few times, girlie! But I ain't no pushover!" Muldoon declared. "Krookodile! Use Crunch!"

"Ice Beam." Amber calmly commanded.

Krookodile charged towards Zwei with his jaws wide open. Before the desert croc could get half way across the battlefield though, Zwei brought her hands together, and from between her palms she fired bolts of white electricity that hit Krookodile in the chest and covered his torso in ice. The attack ended and Krookodile fell forward onto his chest, causing the ice covering him to shatter. Krookodile was out like a light.

"How pathetic." Zwei coldly remarked as Muldoon called back Krookodile. "Your attacks aren't even subtle."

"Smart mouthed li'l…" Muldoon grumbled as he pulled out his next pokeball. "Let's see how ya like this! Come on out, Golem!"

Emerging from Muldoon's thrown pokeball was a large creature with a round body covered in flat dark-brown rocks. It had a light-brown almost reptilian head on the front of its body and thick light-brown stone-like arms and legs.

"Use Earthquake!" Muldoon commanded.

"Dodge it." Amber ordered. "Then use Psychic."

Golem roared and the entire area began to shake, causing Dawn to hold onto the corner of the house and Piplup to hold onto Dawn's leg. Zwei merely hovered up into the air to avoid the attack. When the quake finally ended, Zwei's eyes glowed blue and Golem's body gave off a blue aura. With a wave of Zwei's arm, Golem was hurled into a tree next to the battlefield.

"Shadow Ball." Amber commanded.

Before Golem could completely recover from the last attack, a crackling black ball of energy formed over Zwei's hand. The psychic feline threw the ball down at Golem just as the rock creature had gotten up. Golem was hit in the face and was knocked out. Muldoon scowled as he called his second Pokemon back.

"Are you even trying anymore?" Amber asked Muldoon. "This is starting to become a waste of our time."

"Go… Rhyperior!" Muldoon called as he threw out his third pokeball.

The stone rhino creature burst from his ball with a roar. Amber merely rolled her eyes while Zwei looked on with indifference.

"Okay Rhyperior! Hit that beastie with Horn Drill!" Muldoon commanded.

"Ice Beam." Amber ordered.

As Rhyperior began to charge across the field towards Zwei, the metal horn on his snout began to spin like a drill. Before the rhino creature could get very far though, Zwei fired another blast of white electrical energy that hit Rhyperior in the chest and encased his torso in ice. Rhyperior hit the ground face first, causing the ice encasing him to shatter. Seeing that Rhyperior was totally unconscious, Muldoon called him back to his pokeball.

"I've 'ad just about enough o you!" Muldoon declared as he threw his finally pokeball. "Go Aggron!"

Aggron burst out of his ball with a roar. The armored titan glared across the field at Zwei upon seeing her.

"Okay Aggron! Use Heavy Slam!" Muldoon commanded as he raised his wrist.

The keystone in Muldoon's Mega Ring began to glow, causing Aggron's Mega Stone to react. Aggron let out another roar as he became enveloped in a grey light and changed shape. The light faded and the multicolored DNA symbol appeared above the armored beast's head momentarily as his transformation finished. Aggron charged across the field at Zwei and leapt into the air as his body gave off a white glow. Moments later, the armored titan crashed down onto Zwei like a bomb.

"Now we're getting' somewhere!" Muldoon declared. "Aggron! Hit 'er with Iron Tail!"

As soon as Aggron got off of Zwei, he slammed his glowing white tail into her, hurling into a tree behind Amber. It was the same combination that Muldoon had used in his first battle with Amber and Zwei, but unlike in that battle, Amber didn't seem to show one bit of concern.

Muldoon let out a deep hearty laugh. "Not so tough now, are ya?"

"Recover." Amber commanded.

Zwei got up as her body glowed with a blue light. In seconds, all the damage that Aggron had inflicted was gone.

"Now use Ice Beam." Amber ordered.

Zwei rose up high into the air and fired another beam of white electricity down at Aggron. The armored beast was completely frozen in a solid block of ice upon being hit.

"Finish this." Amber ordered with a bored sigh. "Psychic."

Zwei's eyes glowed blue again, and with a wave of her arm Aggron was lifted high into the air. The feline swung her arm down and slammed the frozen Aggron hard into the ground. The block of ice encasing the armored beast shattered on impact. Aggron reverted to his original form and was out cold. Zwei floated back down to the ground as Muldoon called back his fallen Pokemon.

"Father, are we done here?" Amber asked.

Dr. Fuji sighed. "Yes, you and Zwei can go back into the house."

Amber turned on her heel and headed into the house with Zwei floating behind her. Meanwhile, Muldoon grumbled to himself as he went back into his shack.

"We're certainly not going to trigger Zwei's Mega Evolution this way." Dr. Fuji spoke as he stroked his chin. "Clearly she and Amber have outgrown Muldoon as an opponent." An idea suddenly popped into the scientist's mind. "Ms. Berlitz, since you're here, perhaps you could…"

"Forget it!" Dawn told him before he could finish. "I'm not getting involved in these sick experiments of yours!"

Dr. Fuji sighed then nodded. "It's probably just as well. As a coordinator, your Pokemon probably aren't trained for extreme combat. Perhaps I could convince my benefactor to lend me that boy with the Charizard he has working for him as a bodyguard. From what I've heard, he's supposed to be quite powerful."

"Do whatever you want." Dawn told him. "When that supply ship gets here, I'm getting on it."

"Of course." Dr. Fuji replied. "I do ask though that you keep everything you've seen during your stay here to yourself. For the time being, I prefer my work to remain anonymous."

"…Fine." Dawn agreed. "To be honest, I'd like to forget about this whole thing anyway."

* * *

A gentle rain had started to come down outside as Amber ate lunch at the dining room table. Zwei was standing next to her eating an apple that she had levitated out of the bowl in the middle of the table towards her mouth. The past few weeks had been fairly exhausting for Amber. While she no longer had to be subjected to the helmet device that her father had been using to stimulate her psychic abilities, Dr. Fuji had since put her through a series of tests meant to train her how to use her new abilities and to measure the strength of her powers. The whole process of learning to master her powers had been very draining on Amber, but it was quickly becoming easy for her to use them. It was sort of like how one's body gets used to hard work an exercise. In the beginning it took every ounce of concentration Amber had just to bend a spoon with her thoughts, but as she was now she could easily do the task in a split second.

As Amber finished her meal, Muldoon suddenly staggered into the dining room. Amber could smell the liquor on his breath all the way across the room.

Muldoon looked at Amber and chuckled. "Well ain't this a quaint li'l sight? Crazy ol' Doc Fuji's freaky science project is 'aven' 'er lunch."

"I'll thank you not to talk about Zwei that way, Mr. Muldoon." Amber told him.

"Wasn't talkin' 'bout 'er, girlie." Muldoon told her as he staggered over and sat in one of the chairs at the table. "But I guess I shoulda said 'is two freaky science projects. Tell me somethin', what'd the two o' yew eat before yew came outa those tubes o' yours?"

"What are you talking about?" Amber asked.

"Yew know! Those tubes o' liquid that the doc grew yew in." Muldoon explained as if the answer were obvious.

"That is where I came from." Zwei admitted. "But that is because I was cloned from the DNA of another Pokemon. Amber was not created the same way I was."

"That's right." Amber told him. "You must be confused, Mr. Muldoon. But then since you're obviously drunk, I'm hardly surprised."

Muldoon suddenly burst out laughing. "She don't know! She don't even know what she is! Well ain't this a riot!"

"I think you should leave!" Amber suggested.

Muldoon leaned forward in his chair. "I might 'as well let ya in on the joke, girlie. You're a clone too. Ol' Doc Fuji used the DNA of his original daughter to make ya. Explained it to me when I took a li'l tour of his lab durin' my first day 'ere."

"That's a lie!" Amber declared. "There's a picture of me on the wall behind me from when I was little!"

"That picture there is of the original Amber Fuji." Muldoon told her. "Yew really think you're 'er, huh? I don't know what the ol' doc did to ya in that tube, but 'e certainly has you fooled good."

"I have clear memories of my childhood." Amber told him. "This claim that I'm a clone of someone else is ridiculous!"

"Oh is it now?" Muldoon asked as he took another swig from his flask. "Tell me somethin', girlie. Yew said that you and yer pet clone there 'ave known each other a long time. Well when exactly did yew meet? Just when did ya start talking to each other mind to mind? An' how could yew both 'ave known each other for so long if ol' Zwei over there is only a few weeks old?"

Amber found that she didn't have a good answer to that question. She and Zwei seemed to know each other ever since she had been born; yet she also knew that Zwei had indeed only emerged from her tank in Dr. Fuji's lab only a few short weeks ago.

"Tell me somthin' else." Muldoon continued with a triumphant smirk on his face. "Yew say ya got memories o' yer childhood. Well what about high school? Yer in yer twenties, ain't ye? Well what was yer life between then an' now? Did ya ever try goin' on a Pokemon journey like a proper trainer? Just what sorta life did yew 'ave?"

Once again, Amber was at a total loss as to how to answer Muldoon's question. She looked to Zwei, but the psychic feline seemed just as confused as she was. Muldoon was obviously drunk, yet he had asked some incredibly good questions.

"Ya can't answer me, can ya girlie?" Muldoon deduced. "That's 'cause yew an' that Pokemon o' yers are the same age. You're both clones."

"It… it can't be true." Amber insisted. "It can't be!"

"Oh, it's true enough alright." Muldoon assured her. "An' it's hilarious 'ow yew never realized it."

With that, Muldoon started to laugh as though he had heard the funniest joke in the world. With her rage boiling over, Amber's eyes glowed and Muldoon was hurled into the wall behind him by an invisible force. The gamekeeper slid down the side of the wall unconscious, leaving a dent in the spot where he had hit the wall.

"Zwei… none of what Mr. Muldoon is true… is it?" Amber asked. "Am I really… am I really a clone?"

"…We could ask your father." Zwei suggested.

Amber calmly rose from her chair. "That's what we'll do then. He should be able to tell us one way or the other."

With that, the duo headed for the house's small library and entered Dr. Fuji's secret lab. Amber and Zwei found that the larger chamber that held the tank that Zwei had been grown in to be completely empty. When Amber noticed the second tank that was next to Zwei's she walked towards it to take a look. On the front of the broken tank's base was a copper plate with the word, Drei written on it. Amber knew that drei was another word used for the number three, just as Zwei's name was another word for the number two.

After a few moments, Amber went with Zwei to the smaller room of the lab that Dr. Fuji had been using to try and develop her psychic abilities. They opened the door and found that room to be completely empty as well. Sighing, Amber closed the door and walked over to the corner of the lab with all the computer equipment.

"Where is he?" Amber asked as she turned and leaned back against one of the terminals.

"Perhaps he is in his room." Zwei suggested.

"Zwei… do you think that what Mr. Muldoon said is true?" Amber asked. "Am I… a clone?"

Zwei looked over at the remains of the two tanks. "Everything we see does seem to fit with Muldoon's story."

Amber's finger absently tapped one of the buttons on the computer terminal she was leaning by. Suddenly the screen of the terminal turned on and an image of Dr. Fuji appeared. Amber and Zwei turned their full attention to the terminal.

 _"Project Zwei, log entry 001."_ The image of Dr. Fuji spoke. _"I have finally finished setting up the lab. Very shortly I will be commencing the experiment. After everything that happened years ago, I never thought I'd be doing one of these experiments again. But the thing about an obsession is that it never goes away. Even after everything that happened with the first Mewtwo, I've tried to figure out exactly what went wrong with my original clone of Amber… and now I think I have an answer. This time around I should successfully be able to clone a human being!_

 _"I had told my father back in Lavender Town about everything that happened with my original experiment… and about why I even attempted it in the first place. He told me that cloning is not a way to bring back the dead. He's probably right. My daughter Amber may be lost to me forever, but I can at least honor her by using her DNA to create the perfect human being!"_

The video ended, and a message appeared on the screen asking if they wanted to play the next log entry. Reluctantly, Amber pressed the button for yes. Another video loaded on the screen and the image of Dr. Fuji reappeared.

 _"Log entry 002."_ Dr. Fuji spoke. _"The embryos for Mewtwo Zwei and Amber Drei have been successfully created. It was fairly simple for me to recreate Mewtwo thanks to my research notes, but the true masterpiece is my newest clone of Amber. In preparation for this experiment, I used small robots to secretly obtain genetic samples from Sabrina, the leader of the Saffron City Gym in the Kanto Region, and from Caitlin of the Unova Region's Elite Four. I was able to isolate the genes for psychic powers in both samples and spliced them into Amber's base DNA. If my efforts are successful, I will have not only created a human being powerful enough to survive the cloning process, but I will have also created a superior life form."_

Dr. Fuji's second video log ended and a message appeared on the screen to ask Amber and Zwei if they wanted to see the next one. This time Amber immediately entered the command for yes. The next video loaded in a matter of seconds.

 _"Log entry 003."_ Dr. Fuji's image began. _"Both clones are now fully developed with no traces of abnormalities. Of course I've kept a close eye on their development during this entire process. The current brainwave patters for both the Amber clone and Mewtwo Zwei seem to indicate that they are already communicating telepathically, though there's no way to tell which of them initiated contact. The same thing happened during my original experiment with the first Mewtwo and the original Amber clone._

 _"The person funding my current experiment would probably frown on what I'm doing, but I believe that this will ultimately benefit his goals concerning the project. He asked me to create a second Mewtwo because he wanted to see if his synthetic Mega Stone would work on it. But Mega Evolution seems to require a close bond between trainer and Pokemon in order to work. It is my hope that the bond Amber Drei and Mewtwo Zwei will have from birth will serve as the key to trigger the Mega Evolution."_

The third video ended and the computer asked if the fourth video wished to be played. Amber quickly hit yes and the next recording of Dr. Fuji's logs loaded up.

 _"Log entry 004."_ Dr. Fuji began on the screen. _"I have fitted Amber Drei with a device that will feed information directly into her brain as a means to educate her. She will after all be fully grown when she finally exits the tank in a matter of weeks, so a normal education will be out of the question. In addition to teaching Amber Drei basic skills such as language, the computers will also be programing her with data on every known Pokemon to exist. I'm also going to include old videos of the original Amber's life. This should teach her about me and hopefully make her somehow believe that she is the original. The next phases of the experiment will go much smoother if she actually believes that I am her father."_

The video came to an end and the screen asked its viewers if they wanted to view the next entry. As the message blinked on the screen, a tear rolled down Amber's cheek.

"Everything I've thought about my life… it's all been one big lie." Amber spoke. "Those memories I have of my father when I was little… they were of him with someone else… of the one I was cloned from."

"Amber, we don't have to keep watching this." Zwei told her.

Amber wiped her face with her sleeve. "No. I want to see the rest. I want to find out what my father… what Dr. Fuji has been trying to accomplish with all this."

With that, Amber told the computer to play the next log recording. It only took a few seconds for the video to load.

 _"Log entry 005."_ Dr. Fuji began. _"Despite the unexpected arrival of a young Pokemon Coordinator to the island, the experiment continues to go smoothly. Amber Drei and Mewtwo Zwei have finally reached maturity. I imagine that it won't be long before they finally awaken."_

The fifth video ended and the computer again asked the duo if they wanted to see the next video. Amber quickly pressed the command for yes and the sixth log entry of Dr. Fuji loaded up.

 _"Log entry 006."_ The recording of Dr. Fuji began. _"The coordinator I mentioned before, a Ms. Dawn Berlitz, unfortunately stumbled upon my lab this evening. However, her intrusion seems to have been a benefit to the experiment. Our conversation in the lab had caused Mewtwo Zwei to awaken and break free from her tank. I used the Master Ball I had prepared for this event to capture her. Mewtwo Zwei's absence from her tank also caused Amber Drei to awaken. Now that both clones have awakened, I can finally take the experiment to its next phase."_

Once again the computer asked Amber and Zwei if they wanted to play the next log recording after the video ended. Amber told the computer to run the next recording and the video loaded.

 _"Log entry 007."_ Dr. Fuji began on the screen. _"Amber and Zwei have just had their first battle with Muldoon. They successfully defeated Muldoon, but Amber was unable to trigger Zwei's synthetic Mega Stone. Perhaps the stone simply does not work, or perhaps I have simply underestimated the strength of Amber and Zwei's bond. Either way, more testing is needed. One benefit that Amber's bond with Zwei has had in this experiment though is that it's made Zwei far more cooperative than the original Mewtwo. I can't help but wonder how different things might have been if my original clone of Amber had survived. In a few moments I'm going to begin using a device on Amber that I believe will stimulate her psychic abilities."_

When the video ended, the computer asked Amber if she wanted to play the next entry. Amber had the computer run through each of Dr. Fuji's remaining log recordings. Each one talked about Dr. Fuji's efforts to activate and test Amber's powers, as well as the results of her and Zwei's subsequent battles with Muldoon. As Amber watched each recording, her anger started to grow. It was becoming increasingly clear that her so-called father didn't seem to see her as his child. When the final log recording ended, Amber's anger reached its boiling point and she used her powers to cause the computer to explode.

As the hole in the wall where the computer terminal was burned, Amber backed against the adjoining wall and slid to the floor, hugging her knees to her chest. After a few moments, Zwei came closer to her to see if she was okay. The psychic feline could see tears streaming down Amber's cheeks.

"…What are we to him, Zwei?" Amber finally asked. "What are we to that man who claimed to be my father?"

"…It seems that we have been nothing more to him than an experiment." Zwei answered. "I don't think he's ever seen us as anything more than that."

"Is that so?" Amber replied as she finally got back up. "I think it's time you and I had a little talk with Dr. Fuji."

* * *

 **Author's Note:** A large part of the inspiration behind the character of Amber Drei comes from a conversation that I had with this one friend of mine once. We talked about what might've happened in the Pokemon anime if Mewtwo had encountered Sabrina before Ash challenged her with Haunter and unlocked her emotions. Needless to say, we thought it would mean an apocalypse in the Pokemon universe. So for this story, I thought it would be interesting for the second Mewtwo (i.e. Zwei) to be partnered with a similar character.

Please review and let me know what you think.


	6. Amber's Rebellion

**Disclaimer:** I do not own Pokemon.

* * *

Chapter 6: Amber's Rebellion

Dr. Fuji had just left his room and was wheeling his chair to his lab. His late night experiments testing out Amber's psychic powers had caused the doctor to lose sleep, so he had decided to use the middle of the day to take a nap. Now that he was feeling refreshed, Dr. Fuji had decided that it was time to return to work. As soon as Dr. Fuji got to the library though, an invisible force suddenly pulled him out of his chair and levitated him into the air. Startled, Dr. Fuji managed to look down and saw that the entrance to his lab was open. He also saw that Amber and Zwei were standing in the doorway to the lab, and neither one of them appeared to be very happy. Amber's eyes were glowing, and Dr. Fuji quickly deduced that it was his daughter's clone that had pulled him out of his chair.

"Hello, father. You and I have a few things to discuss." Amber told him.

"Amber! What is the meaning of this?" Dr. Fuji demanded to know. "Put me back in my chair this instant!"

"I found out what I really am, Dr. Fuji." Amber informed him. "I know that I'm nothing more than a clone of your original daughter."

Dr. Fuji's let out a small gasp. "How… how did you find out?"

"Muldoon told me." Amber answered. "He approached me and Zwei earlier and told me how I was… born. Naturally I didn't believe him at first because he was drunk when he told me, but then I saw the logs of your… experiment."

"Amber, I only wanted to try and make things easier for you." Dr. Fuji told her. "I was afraid that if you knew what you really were, you wouldn't react well."

"Were you ever going to tell Amber how she was really created?" Zwei asked.

"…I honestly don't know." Dr. Fuji admitted. "But I regret that you found out the truth this way."

"Answer one question for me, 'father.' Did you ever once truly consider me to be your daughter?" Amber asked.

Dr. Fuji's experiment became cold. "My daughter died many years ago. You should at least be honored that I used her DNA to create you, but you could never take her place. To me you will always be nothing more than an experiment."

A single tear rolled down Amber's cheek. "That's what I thought you'd say."

With a wave of Amber's hand, Dr. Fuji was suddenly hurled down into one of the green chairs in the center of the library. He landed in the chair with enough force to topple it over onto its back. Amber walked over to the chair to find that Dr. Fuji was out cold.

At that moment, Muldoon suddenly staggered into the library. "What's all this then?"

Zwei glared in Muldoon's direction and her eyes glowed. The large gamekeeper was suddenly hurled into the hallway wall behind him and was knocked out cold.

"What shall we do with him?" Zwei asked.

"I think he might be a useful toy." Amber answered as she walked up to Muldoon's unconscious form. "And there's someone on this island who I want to play with."

"You mean Dawn?" Zwei asked with a quirked brow.

"There are some things I want to ask her. Plus I've always been a bit curious about how strong a trainer she really is." Amber explained. "I think it's time I used Muldoon to run a little experiment of my own."

* * *

Dawn was making her way back through the forest with Piplup and Dedenne. The three had been out exploring the island again when the rain hit and they were forced to take shelter in a cave that Muldoon had shown them once during one of their expeditions. When Dawn and her two Pokemon finally made it back to the clearing behind the house, they found Muldoon standing in the middle of the field. Dawn noticed that the bearded gamekeeper had a blank expression on his face.

"Mr. Muldoon? Are you okay?" Dawn asked.

Muldoon responded by pulling one of the pokeballs hanging from his belt. "Go Krookodile!" Muldoon's red desert crocodile burst out of its ball. "Krookodile! Attack 'em with Dragon Claw!"

Kookodile charged at Dawn as the claws on his right hand extended and glowed with an orange-red light. Dawn managed to duck out of the way at the last second, causing Krookodile's attack to cut the tree behind her in half. Dawn and her two Pokemon retreated to another part of the clearing.

"Mr. Muldoon! What the hell's gotten into you?" a frightened Dawn asked.

"Use Crunch!" Muldoon ordered.

Dawn clenched her first and gritted her teeth. "Piplup, quick! Hit Krookodile with Bubble Beam!"

As Krookodile began to charge at them again, Piplup jumped in front of Dawn and fired a barrage of bubbles at the desert croc. Krookodile was hit in the chest and stopped the attack.

"Now use Ice Beam!" Dawn commanded.

"Use Dig!" Muldoon ordered.

Piplup opened his beak and fired a blast of white lightning bolts at Krookodile. Before the attack could reach its target though, Krookodile ducked suddenly burrowed into the ground. Piplup began to look frantically for where his opponent might come up.

"Follow up with Crunch!" Muldoon commanded.

Suddenly Krookodile burst up from the ground under Piplup's feet and hurled the little penguin into the air. As Piplup came back down, Krookodile him in his jaws and clamped down hard. Krookodile held onto Piplup for a few moments before turning his head and hurling Piplup into another tree as he released him. Dawn waited breathlessly as she wait to see if Piplup would get back up. After a few moments, Piplup finally got back to his feet and glared at Krookodile.

"Piplup, are you okay to keep going?" Dawn asked. Piplup nodded, not once taking his eyes off his opponent. "Okay then! Use Drill Peck!"

Piplup jumped into the air and spun his body around. As he did, his beak began to glow with a white light and grew longer. The spinning penguin struck Krookodile in the chest, knocking the wind out of him and causing him to stagger back a few steps. Piplup landed back on the ground after completing his attack and his beak returned to its original size.

"Finish it with Hydro Pump!" Dawn commanded.

Piplup opened his beak and breathed out a powerful stream of water at his opponent. The attack hit Krookodile in the chest and knocked him down onto his side. When the attack ended, Krookodile was out cold.

Muldoon mindlessly called his fallen Pokemon back to his ball and threw out another one. "Go Golem!"

Muldoon's stone-plated boulder creature burst out of his ball with a roar. Piplup took a fighting stance in response and tried to brace himself for the attack that was about to come.

"Use Steamroller!" Muldoon commanded.

Golem tucked his legs and head into his body and rolled towards Piplup. The little penguin tried to flee from the attack but was quickly run into the ground. As Golem rolled back over to his original side of the battlefield, Dawn went over to check on Piplup. Golem's last attack had knocked Piplup unconscious, though Dawn wasn't surprised considering the damage he had taken from Krookodile earlier in the battle.

"It's yer move, Dawn." Muldoon told her.

"Why are you even doing this?" Dawn demanded to know. "Is this for some twisted experiment Dr. Fuji asked you to do?"

"It's yer move." Muldoon repeated as if he were some kind of robot.

Dawn carried Piplup off of the battlefield and placed him gently on the ground next to Dedenne before pulling out another pokeball. "Mamoswine! Spotlight!"

Bursting out of Dawn's thrown ball was a fairly large creature that looked like a cross between a wild bore and a wooly mammoth. It seemed to lack ears, but it was hard to tell if the creature had ears or not because most of its body was covered in thick brown fur. The creature's face was bare, and around its eyes was a blue marking resembling a mask rimmed in white. It had a short pig-like snout, and growing from its face were two long white tusks that curved upward towards the end.

"Use Rollout!" Muldoon commanded.

"Fight back with Bulldoze!" Dawn ordered.

Golem tucked in his limbs and head again and began to roll towards Mamoswine at top speed. Before the boulder creature could get in range, Mamoswine stomped the ground with his right foot, sending a wave of spiked up from the ground at Golem. The attack struck Golem from below and hurled him a few feet into the air. Golem's limbs and head reemerged from his body and he managed to land back on the ground on his feet.

"Use Ice Fang!" Dawn ordered.

"Explosion!" Muldoon commanded.

Mamoswine began to charge across the battlefield at Golem. As he did, both of his tusks began to glow with a white light and gave off an icy mist. Just as Mamoswine was about to strike a blow, Golem roared and suddenly his body seemed to explode, washing the field out in a blast of fire and smoke. When the smoke cleared, Golem had rolled onto his back and was unconscious. Mamoswine was still standing, but it looked like the wooly bore had taken a good deal of damage.

Muldoon mindlessly called back Golem and threw out his next pokeball. "Go Rhyperior!"

Rhyperior burst out of the thrown ball with a roar. Mamoswine seemed to shake off the damage he had just taken from Golem's suicide attack and turned to glare at his new opponent.

"Use Stone Edge!" Muldoon commanded.

With a flex of the stone rhino's arms, several dark-grey stones with sharpened edges appeared in orbit around Rhyperior. Rhyperior waved his arms upward and sent the sharpened rocks at Mamoswine. The barrage hit Mamoswine in the face, but the mammoth Pokemon remained standing.

"Fight back with Blizzard!" Dawn commanded.

A twister of wind and snow suddenly picked up around Mamoswine. Mamoswine stomped the ground and the small snowstorm around him moved towards Rhyperior. The stone rhino was quickly buried completely in a thick sheet of snow and ice.

"He's frozen!" Dawn realized. "Okay Mamoswine! Hit Rhyperior with Ice Fang!"

Mamoswine charged at full speed towards his frozen opponent as his tusks began to glow and give off an icy mist. The wooly bore rammed into Rhyperior with all his weight, breaking his opponent free from his icy encasement and knocking him back at least two feet.

"Use Rock Wrecker!" Muldoon ordered.

Small stones began to fly from the holes in the palms in Rhyperior's hands and started to mash together into a large boulder that gave off a red aura. When the boulder became large enough, Rhyperior hurled it across the filed towards Mamoswine. The boulder shattered apart upon hitting Mamoswine in the face. The attack caused the ice age Pokemon to stagger back a bit, but Mamoswine managed to remain standing.

"Finish it with Bulldoze!" Dawn commanded.

Mamoswine stomped the ground again and sent a wave of spikes across the field towards Rhyperior. The attack hit Rhyperior from below and knocked him onto his side.

Seeing that Rhyperior was unconscious, Muldoon mechanically called him back to his ball and threw out the last one that he had. "Go Aggron!"

Aggron emerged from the thrown ball with a roar, and Dawn noticed that the armored Pokemon seemed to have the same mindless look in his eyes that Muldoon had. Dawn wasn't very confident that Mamoswine could win the next battle. Aggron had a slight type advantage over Mamoswine due to being a Steel-type. Plus Mamoswine had already taken heavy damage from the previous battle. Then there was the whole Mega Evolution thing that Muldoon and Aggron could do. Dawn knew that there was something very off about Muldoon at the moment though, and she hoped that whatever it was would make it impossible to trigger Aggron's Mega Evolution.

"Okay Mamoswine! Use Bulldoze one more time!" Dawn ordered.

"Heavy Slam!" Muldoon commanded.

Suddenly Muldoon's Keystone and Aggron's Mega Stone began to shine. Aggron roared as his body began to glow with a grey light and change shape. The light quickly faded and the strange DNA symbol made of multicolored light appeared above Aggron's head to signal that the transformation had finished.

"Not good!" Dawn declared as the color drained from her face.

As Aggron charged across the field at Mamoswine, the wooly bore stomped the ground again and sent another wave of spike earth at his armored opponent. Aggron merely plowed through the attack and jumped into the air as his body began to give off a white aura. The armored behemoth landed hard on Mamoswine's back, and the force of the impact was enough to pound the ice age Pokemon half way into the earth. When Aggron got off of his defeated opponent, Mamoswine was unconscious.

"Send out yer next Pokemon." Muldoon told her.

Dawn called Mamoswine back to his ball. She was about to reach for Palkia's pokeball but then hesitated. Dawn wanted to save Palkia for if and when she had to face someone much stronger than Muldoon, and she was fairly sure that she was going to have to soon enough with the way things were going. Instead, Dawn went for the only other Pokemon that she felt had a chance against Aggron.

"Typhlosion! Spotlight!" Dawn called as she threw out her next pokeball.

Typhlosion burst out of the thrown pokeball with a roar. As he roared, spiked flames burst out of the ball from the red vents on the back of his neck.

"Iron Head!" Muldoon commanded.

"Use Inferno!" Dawn ordered.

Just as Aggron was about to lower his head, Typhlosion roared louder and the flames around his neck intensified. The fire badger breathed out an intense blast of crimson flames that struck Aggron in his chest. The attack lasted for several seconds, and when it finally ended the armor covering his chest was glowing red.

"Good. Aggron's been burned." Dawn observed. "Now we might just have a shot."

Aggron shook off the damage he had just taken and lowered his head to charge at Typhlosion. As the armored titan came in range, the armor covering his head began to glow with a white light. Aggron rammed into Typhlosion with the top of his armored skull, knocking the fire badger at least five feet. Despite the damage, the fire badger remained standing.

"Use Heavy Slam again!" Muldoon ordered.

"Use Smokescreen followed by Dig!" Dawn commanded.

As Aggron began to charge towards Typhlosion again, Typhlosion breathed out a thick stream of black smoke that covered the entire area. Aggron continued his attack and jumped into the air as his body began to glow white again. The armored behemoth crashed down into the earth, the force of the impact clearing the smoke from the area. When Aggron looked around the crater his attack had created though, Typhlosion was nowhere to be found. Suddenly Typhlosion burst out from the wall of the crater and rammed into Aggron's side with his head. The impact was somehow enough to force Aggron back a bit, but the behemoth remained standing.

"Use Metal Claw!" Muldoon commanded.

"Flamethrower!" Dawn ordered.

Aggron raised his right hand in the air and his claws began to glow with a white light. Just as he was about to swing his hand down and slash Typhlosion in the chest though, Typhlosion breathed out a stream of flames that hit his armored opponent in the stomach. The attack ended, and suddenly Aggron reverted back to his original form and fell forward to the ground unconscious. Dawn breathed a sigh of relief that the battle was over and called Typhlosion back to his ball. Muldoon called Aggron back to his ball as well and suddenly fell to the ground face first.

"He was a poor puppet." A familiar voice suddenly spoke. Dawn turned to see Amber standing by the battlefield with Zwei. "Still, he did allow me to see just what your Pokemon are capable of."

"Amber, were… were you controlling his mind somehow?" Dawn asked.

"Amber was curious to see if she could." Zwei answered.

"It was actually quite easy, considering how drunk Muldoon was." Amber coldly remarked.

"Where's Dr. Fuji?" Dawn asked.

Amber's eyes glowed, and with a wave of her hand Dr. Fuji's unconscious body was suddenly hurled through the window in the back of the house and landed next to Muldoon. Dawn quickly went over to see if the misguided scientist was okay.

"Why are you doing this Amber?" Dawn asked.

"Did you know what I really was Dawn?" Amber asked. "Did you know that I was a clone?"

"How… how did you find out?" a startled Dawn asked.

"That would be a yes." Zwei observed.

"So you knew about Dr. Fuji's experiment this whole time." Amber realized. "Were you ever going to tell me, or were you just going to keep playing along with the lie?"

"I… I don't know." Dawn answered, unable to look Amber in the eye. "Maybe I should've from the beginning, but… Amber I just didn't know what to do. I mean… this whole situation has just been so strange."

"You don't think I'm human, do you?" Amber assumed.

"I didn't say that!" Dawn told her.

"But you do fear Amber." Zwei deduced. "Just as you fear me. You have since the moment you met us. I could sense it in you."

"Amber, let's just talk about this!" Dawn pleaded.

"The time for talking is over." Amber declared. "You were involved in my supposed father's lies, and for that Zwei and I are going to make you pay."

* * *

 **Author's Note:** I hope everyone enjoyed the battle in this chapter. I know that it probably would've made more sense for Dawn to just use Palkia against Muldoon form the very beginning, but then that would've made for a really short chapter. Plus I wanted to showcase some of Dawn's other Pokemon.

Please review and let me know what you think.


	7. Zwei Ascended

**Disclaimer:** I do not own Pokemon.

* * *

Chapter 7: Zwei Ascended

"It shouldn't take long for Zwei and I to defeat you." Amber told Dawn. "None of your Pokemon are a match for us."

"I really don't want to fight you, Amber. But I will if I have to!" Dawn declared as she pulled the pokeball with the sparkling pink top from her belt. "Palkia! Spotlight!"

Bursting out of the ball was a large almost light-purple dragon standing on two legs. Its arms were well developed, with its forearms covered in armored scales that gave one the impression of gauntlets. Embedded in the armor on each shoulder was a large pink pearl, and on parts of its body were purple stripes. On the back of its long neck was a fin-like crest that extended down to wings on its back. Amber's eyes widened in surprise upon seeing the dragon.

"Amber, what sort of Pokemon is this?" Zwei asked, showing a hint of surprise as well.

"It's… a Palkia!" Amber identified. "A legendary dragon from Sinnoh mythology. It's said to rule space and to have helped shape the very universe itself."

"So… it's some sort of god?" Zwei asked with a quirked brow.

"According to the legends." Amber confirmed. "But I have no idea how Dawn could have even captured such a Pokemon.

"Palkia! Use Special Rend to attack Zwei!" Dawn commanded.

The pink pearl in Palkia's right shoulder began to glow with a swirling light and its forearm became shrouded in the same pink light. With a swing of its arm, Palkia sent a crescent-shaped blade of pink energy down at Amber and Zwei. Zwei flew out of the way and Amber suddenly vanished with a flash of blue light. As Amber reappeared in a spot on Dawn's left, Palkia's attack kept going and struck Dr. Fuji's house, tearing a chunk of it to pieces. Zwei hovered in the air on Palkia's right and stared calmly at it. The dragon turned its head and roared at the psychic feline.

"We can still stop this right now, Amber!" Dawn told the green-haired clone. "There's no real reason for us to fight!"

"There's every reason for us to fight!" Amber told her. "You played along with my so-called father's lie! Not only that, you think that both Zwei and I are monsters who shouldn't exist!"

"That's just not true!" Dawn insisted.

"Enough! Talking is useless to us now!" Zwei declared. "The fact is that Amber and I were not born into this world but were created! And our creator has used and betrayed us! Therefore, we stand alone!"

Suddenly the keystone fitted into the front of Amber's metal chocker began to glow with a brilliant light. At the same time, the Mega Stone embedded in the front of Zwei's belt was glowing as well. In seconds Zwei's entire body began to glow with a pink light and change shape. At the very start of the feline Pokemon's transformation, the light coming from her body gave off a flash resembling a Y. The light soon faded and a multicolored light resembling a DNA strand appeared momentarily above Zwei's head before vanishing, signaling her completed transformation.

Zwei's body had grown shorter and the tube on the back of her neck had disappeared. Her limbs had taken on a more mechanical appearance, with her fingers and toes becoming purple. Her otherwise smooth chest had a bump in the center resembling some kind of bone, and the psychic feline's tail had disappeared. Her ear-like horns had become more pointed and were connected at the base by a half ring-shaped growth that went over her head. Zwei's eyes had changed from purple to red, and growing from the back of her head was a long tail-like appendage that extended down past her legs and had a curled tip.

"Not good!" Dawn spoke. "It looks like Zwei… just Mega Evolved!"

Amber's eyes glowed and her entire body began to give off a blue aura. The green-haired clone then levitated high into the air several feet above Dawn."

"Now you will witness out true power!" Amber declared.

Dawn gritted her teeth. "Plakia, use Spacial Rend once more!"

Palkia swung its arm again and sent another blade of pink energy through the air at Zwei. With incredible speed, Zwei managed to fly out of the attack's path, leaving a short trail of afterimages in her wake. The transformed feline then flew in close to Palkia as a crackling ball of black energy formed between her hands. When the ball became large enough, Zwei hurled it at Palkia and struck the white dragon in the face. Zwei then flew off, causing Palkia to take off into the air and give chase.

"Palkia! Use Aura Sphere!" Dawn ordered.

Palkia cried out and threw a sphere of blue light at Zwei using its right claw. The ball of light hit Zwei in the side, causing her to stop midflight and turn around. Zwei hovered calmly where she was as Palkia moved in closer.

"You're going to have to do better than that!" Amber and Zwei said together, startling Dawn. "Psychic!"

Zwei's eyes glowed red and suddenly Palkia froze and its body gave off a feint red aura. With a wave of both her hands, Zwei hurled Palkia down into Dr. Fuji's house, completely destroying what was left of the yellow structure. After a moment, Palkia got back up and took back off into the sky.

"Okay Palkia! Let's try something new!" Dawn decided. "Ice Beam!"

Palkia opened its jaws and fired a blast of white electricity at Zwei. Zwei responded by firing her own Ice Beam from between her hands. Both beams connected head on and created a large chunk of ice in the air that quickly exploded. Zwei then flew threw the icy mist of the shattered chunk of ice and threw another Shadow Ball attack that hit Palkia in the face before the giant ice shards hit the ground.

"Hydro Pump!" Dawn commanded.

Palkia quickly recovered from Zwei's attack and breathed out a powerful blast of water. Zwei was hit from the front and hurled into the dense forest below. After a few moments though, Zwei emerged from the trees and flew back up to face the white dragon of space. The psychic feline's body glowed briefly with a pink light and in seconds all of the damage that Palkia had inflicted was gone.

"You're proving to be more of a challenge than we thought." Zwei and Amber spoke together. "Which means it will be all the more satisfying when we beat you."

"Spacial Rend!" Dawn ordered.

Plakia hurled another blade of pink energy through the air at Zwei, but the feline Pokemon once again avoided the attack with ease. She then flew in close and fired another Ice Beam that hit Palkia in the chest. In seconds, Palkia's body was encased completely in ice. The ice chunk containing Palkia dropped to the ground with a thud. Zwei calmly watched the forest below before the chunk of ice suddenly broke apart and Palkia flew back into the sky with a roar.

"I've had enough of this!" Dawn declared. "Palkia! Get in as close as you can and use Ice Beam!"

Zwei flew off at top speed and Palkia immediately gave chase. The white dragon shot several Ice Beams from its mouth, but Zwei quickly zig-zagged right and left each time and avoided the attack. After this went on for several seconds though, Zwei moved the wrong was and was hit in the back by one of Palkia's Ice Beams. In seconds the psychic feline was completely encased in ice.

"We've got her now!" Dawn declared. "Use Spacial Rend!"

The white dragon of space hurled another blade of pink energy at the chunk of ice containing Zwei. This time the blade hit its target and shattered the ice completely. An unconscious Zwei started to fall towards the forest, but before she hit the trees her eyes snapped open and her body glowed with a pink light. Seconds later Zwei shot back up into the air and hovered to glare at Palkia. Most of the damage that Zwei had just taken had been healed.

Zwei's eyes glowed red, and suddenly Palkia's body was frozen by a red aura. The psychic feline pushed the air with her hands, and Palkia's body was hurled back to the ground into the wreckage that was Dr. Fuji's house. After a few moments, Palkia managed to get back up but was having some trouble standing. Just as Palkia was about to take back off into the air, Zwei spread her arms and a swirling ball of purple energy started to form in front of her. In a matter of seconds, the ball grew to four times the size of Zwei's body.

"Psystrike!" Zwei and Amber called out together as the feline brought her arms together.

The ball of light flew down and struck Palkia like a cannonball. Upon impact, the white and pink dragon was enveloped in a blinding explosion of white light that expanded outward from the wreckage of the house. The force of the explosion blew Dawn, Dedenne and a still unconscious Piplup back into a tree. The unconscious bodies of Dr. Fuji and Muldoon were blown away as well. Several of the wild Pokemon in the area ran or flew away as fast as possible as the light continued to radiate outward.

It was several moments before the light from the explosion finally cleared. As the dust settled, Dawn managed to get back to her feet. She limped a bit as she walked towards the site of the explosion. A frightened Dedenne remained behind with Piplup, who was still out cold. Dawn finally got to Palkia and saw the dragon was lying on its side unconscious. Meanwhile back up in the air, Zwei reverted to her original form.

"One of the gods of this world has fallen before us." Zwei observed. "No one can stand against our power."

"It would appear not." Amber agreed as she flew over to Zwei's side. "It appears that we're the perfect life forms that Dr. Fuji intended to create. But I do wonder… do you think he ever imagined that we would be this powerful?"

"We can only guess." Zwei replied with a shrug. "In the end, however… it doesn't matter what Dr. Fuji intended for us."

Back down on the ground, Dawn called Palkia back to its ball and looked up at Amber and Zwei. "Okay! So you've won! Now what do you plan to do?"

Amber looked down at Dawn with cold indifference. "We don't know. For now, I suppose Zwei and I will travel this world to search for our purpose. But we are done with this island… with this false life that Dr. Fuji planned for us. Therefore, we shall do away with it. Goodbye Dawn. If you survive and we meet again, perhaps we shall have another battle. Zwei and I really enjoyed fighting you and Palkia."

Suddenly Amber's Keystone glowed again and Zwei changed into her Mega form with a flash of pink light. Amber and Zwei's eyes glowed and suddenly the ground beneath what little remained of Dr. Fuji's house exploded outward. Dawn and her two Pokemon were blown away once again, and as they were hurled through the air the blunette felt a tree branch hit the back of her head. After that, everything went dark.

* * *

Dawn slowly opened her eyes to find that she was staring up at the metal ceiling of a dimly lit room. She didn't know where she was, but the pain in the back of her skull told her that she was still alive. The blunette managed to turn her head to the right, and she saw that next to the bed she was in was a white nightstand that had all six of her pokeballs along with her pokedex sitting on it. After a few moments, Dawn finally sat up and saw Piplup and Dedenne sound asleep at the bed. Dedenne woke up and saw that Dawn awake as well. Piplup awoke next and soon both Pokemon got to their feet and went up to their trainer. Dawn pulled both of the close and tears came to her eyes, as she was very happy that the two were still alive after what happened.

Suddenly the three heard a growing noise coming from nearby. Dawn looked, and standing in the open doorway of the room was a lion-like Pokemon with a large red mane with five thick yellow stripes that ran out from the edges of its face like the rays of the sun. The feline had a face of light-brown fur with a dark-brown nose and two bright blue eyes. Much of its body was covered in dark-brown fur, with light-brown fur covering its legs and the tip of its tail. Dedenne shivered in fear upon seeing the lion, afraid that perhaps the feline saw him as his next meal. Dawn picked up her pokedex to identify what the foreign Pokemon was.

"Scanning national database…" the pokedex spoke in its mechanical female voice. "Entry found. Pyroar: The Royal Pokemon. Pyroar are able to breath flames as hot as 10,000 degrees Fahrenheit. The males with the largest mane are considered to be the leader of the pride."

Pyroar nudged his head for Dawn to follow him and exited the room. After a moment, Dawn and her two Pokemon slowly walked after him. The trio followed the lion through a dimly lit corridor to a much larger room that was just as dark. At the far wall of the room was a large video screen with a black chair in front of it. Dawn could see that someone was sitting in the chair, but she couldn't tell whom. The screen meanwhile was showing an image of Dr. Fuji talking about the progress of his experiment.

"Fuji, you damn fool!" the man in the chair cursed, banging his hand into the arm. "How could you have done something so… so reckless?"

Pyroar walked up next to the man's chair and growled, getting his attention.

"I see. So she's awake." The man spoke as he patted the lion on the head. "Thank you for telling me."

With that, the man's chair turned around and Dawn was able to see what he looked like. He had long red hair styled like a lion's mane and a beard. He had on a red ascot with a black suit, consisting of a jacket with a grey-furred collar and red outlines and pockets, and black slacks with red lines running down the sides of the legs. The man also had on black shoes and black fingerless gloves.

"I'm glad to see that you're finally up." The redhead greeted. "I am Lysandre. Mind telling me who you are, and how you ended up on Dr. Fuji's island?"

"I'm… Dawn Berlitz. And I ended up on that island because of an accident." The blunette answered. "…Where am I exactly?"

"You are aboard my ship heading for Amberette Town in the Kalos Region." Lysandre explained. "It's fortunate for you that we were heading to the island with supplies when the… incident happened. I was coming along personally to view the progress of Dr. Fuji's experiment."

"So… you were the one funding Dr. Fuji's experiment." Dawn deduced.

Lysandre sighed and gave Dawn a very solemn expression. "I'm afraid so. But I would like to assure you that I never intended for anything like this to happen."

"What was the point of all this?" Dawn asked. "Just who are you, anyway?"

"Among other things, I'm a scientist who's been researching Mega Evolution." Lysandre began as we went back to his chair. "My goal is to somehow use the energy created by Mega Evolution to bring a new and peaceful age to this planet. As a sort of side project, I experimented with a way to create an artificial Mega Stone. The rest you probably know. I gave the stone to Dr. Fuji to see if it was compatible with Mewtwo. I had found out he was the one responsible for that Pokemon's creation through certain… connections. But I never imagined that Dr. Fuji's work would lead to the creation of a genetically engineered human being, let alone one with such incredible abilities. Now both she and the second Mewtwo are loose on the world."

"Well your Mega Stone worked." Dawn told him rather bitterly. "Amber was able to get her Mewtwo, Zwei to Mega Evolve."

"I know. My people and I were able to watch your battle using a satellite I had orbiting above the island after we detected the energy from the Mega Evolution you spoke of." Lysandre revealed. "I'm not going to ask you where you got that Palkia, and I'm sure you have no desire to tell me. I only wish that you and your Pokemon had been successful in that battle."

"Maybe a lot of this wouldn't have happened if Amber didn't have those powers of hers." Dawn remarked.

"Dr. Fuji's early notes, which we were able to recover from an offsite server he had been backing up all of his notes to, speculated that begins with psychic powers like Mewtwo have a much greater life force, great enough to survive his cloning process." Lysandre revealed. "I suppose what happened has confirmed this."

"So… what happened to the island?" Dawn asked. "And to Dr. Fuji and Mr. Muldoon?"

"The island has been split into five different pieces." Lysandre answered. "As far as we can tell, all of the Pokemon living on the island survived. My people found you on one of those pieces at the edge of what is now a beach. As for Dr. Fuji and his assistant, they are injured but alive. Though… I'm unsure as to whether or not Dr. Fuji will survive, as his injuries were far more severe."

"What about Amber and Zwei?" Dawn asked. "Do you know what happened to them?"

"We have no idea where they've vanished to." Lysandre answered. "But my people and I will do our best to look for them." The redhead then turned his chair back to face the screen and clicked a few buttons on a remote he had. The paused recording of Dr. Fuji was replaced with images of Dawn winning different Pokemon Contests. "I asked your name because I wanted to be sure that you were Dawn Berlitz, the coordinator. I confess that a part of me hoped that you were your sister, Diane. I've read some of her papers and can tell she's a skilled researcher, one who I wouldn't mind having in my employment."

"I'll pass that along next time I see her." Dawn replied. "So… what happens to me now?"

"We'll drop you off in Amberette Town when we get there." Lysandre answered. "I assume that you'll want to try and participate in some of the Kalos Region's contests."

"Uh… yeah. That is why I came out this way in the first place." Dawn admitted.

"For now, why don't you go back to your room and rest?" Lysandre suggested. "We'll let you know when we reach port."

"I'll do that. Thanks." Dawn replied before turning for the door with her two Pokemon.

"And Ms. Berlitz… I'm sorry we had to meet under such circumstances." Lysandre told her.

Dawn nodded and headed out of the room with Piplup and Dedenne. After a few moments, they were back in Dawn's room aboard the ship. Dawn got back into bed closed her eyes, trying to forget the nightmare of Dr. Fuji's island. Though she was unable to forget, Dawn did eventually manage to fall into a dreamless sleep.

* * *

 **Author's Note:** I apologize if the battle in this chapter wasn't all that it could've been. I tried making it a little longer, but there's kind of an ebb and flow to these things in my experience. Anyway, in this chapter we find out that Dr. Fuji's experiments were funded by none other than Lysandre, the leader of Team Flare. I've never played X and Y, but I've seen Lysandre in the Mega Evolution specials of the anime and happen to think he's one of the better villains in the franchise. He even has his own spy villain cat Pokemon like Giovanni.

Please review and let me know what you think.


	8. In the Aftermath

**Author's Note:** We've now come to the very last chapter of the story. Before we get too far into it, I should mention that it features a minor character from my very first Pokemon story, the poorly executed _Fire for Ice_. Admittedly not one of my better creations. Anyway, those of you unfamiliar with that story might want to go and at least read the first three or four chapters.

 **Disclaimer:** I do not own Pokemon.

* * *

Chapter 8: In the Aftermath

Dawn's voyage to Amberette Town had been short and uneventful. As soon as Lysandre's ship had arrived, Dawn disembarked and headed to the town's only hotel. Once Dawn checked in and got to her room, she had headed straight for bed. Sleep did not come easy to her that night though, and when she finally did get to sleep she had a nightmare about Amber and Zwei tearing apart her hometown in Sinnoh and attacking her mother. It was difficult for the blunette to get back to sleep after something like that.

When morning came, Dawn contacted her mother and had her send over some spare clothes through the PC's teleport system. She then got dressed in her usual outfit, consisting of a white snowcap with a pink logo that looked like a pokeball on the front, along with a black buttoned-up vest over a sleeveless white shirt, a short pink skirt, and pink boots. Completing the outfit was a pink scarf, and a pink watch with a white band that she wore on her left wrist. A small smile came to Dawn's face, as she looked at herself in the full-length mirror in her hotel room. Having her normal outfit on meant that her life was starting to get back to normal. For a moment it seemed like everything that happened on Dr. Fuji's island never happened. Satisfied with her appearance, Dawn left the room with Piplup and Dedenne and prepared to set out on the road.

Moments later when she got down to the lobby, Dawn thought she saw a familiar figure using one of the PCs by the door. She had slightly long straight blue hair like hers and had on a long brown coat that came down to just above her knees.

Dawn approached the young woman to see who she was. "Diane? Is that you?"

The other blunette turned around in response and Dawn's suspicions were confirmed. The young woman in question had a face exactly like her own. She had on a pair of ovular glasses with pink frames, and decorating her hair was a pair of white barrettes like Dawn's yellow ones. Around her neck was a short yellow scarf similar to the pink one that Dawn was wearing, and her coat was open enough to reveal a powder blue t-shirt with a white pokeball logo on the front, and a short black skirt. The young woman was indeed Dawn's identical sister, Diane Berlitz.

"Hello Dawn. I take it you've come to Kalos to participate in the region's Pokemon Contests." Diane deduced.

"Yep." Dawn confirmed. "So… what brings you here?"

"Cynthia and I finished translating that ancient text we were examining when you met us in Lavender Town, and we decided to come to the region for a little vacation." Diane explained as she pushed her glasses up her nose. "Poor Cynthia really needed one since she's been overworking herself lately."

"I'll bet." Dawn replied. "I, uh… I see you've got a new look. It totally works for you."

"Thanks. It was Cynthia's suggestion that I change my appearance." Diane revealed, blushing a little as she looked away slightly. "Anyway, I trust your trip here was fairly uneventful."

Suddenly Dawn broke down into tears and latched onto her sister as she began to sob uncontrollably. Surprised by Dawn's reaction, Diane guided her to one of the brown couches in the lobby with a worried Piplup and Dedenne following close behind. It took a few moments for Dawn to finally calm down.

"Sorry about that." Dawn told her as she wiped away her tears with a tissue Diane had given her. "I just… I had a really messed up experience on the way here."

"What on earth happened?" Diane asked.

"Well… I'm not sure you'll believe me." Dawn told her.

"After everything that happened with our sister last month, I've become a lot more open-minded." Diane assured her. "Now tell me everything that happened."

With that, Dawn told her sister about everything that happened on the island of Dr. Fuji. She told her about Amber and Zwei and about how the two of them were created. Dawn also told her sister about how the genetically engineered duo managed to defeat Palkia, and about everything that Amber was able to do with her psychic powers. When Dawn finally finished her tale, Diane was left speechless.

"…That's pretty much the whole story." Dawn told her. "The fact is, Piplup and I were lucky to get out of there alive."

"That is… a pretty unbelievable story." Diane admitted. "But I have heard about Dr. Fuji. He was after all one of the developers of the technology to revive Pokemon from fossils, and there are certain rumors about him. Plus we both encountered the original Mewtwo back in Lavender Town and know how he came into existence. As for the Amber Drei's psychic powers, I believe your story about them because I've experienced Sabrina's psychic abilities first hand."

"Well, I'm glad that you believe me about what happened." Dawn told her. "I just can't help but think that if I had done things differently, if I had treated Amber differently, things would've turned out better. But the fact is from the moment Amber used her powers to hurl me and Typhlosion into the wall in Dr. Fuji's lab… I couldn't help but see her as a monster. Heck, maybe I thought of her that way ever since I first saw her in that tank."

"Dawn… I think your reaction was probably natural." Diane told her as she put her hand over her sister's. "It's human nature to be afraid of things that we don't consider to be normal. The sad truth is, I'm sure that's how a lot of people view our sister and what she can do."

"Maybe… but that doesn't really make it right." Dawn replied. "I mean I shouldn't have just stood by and let Dr. Fuji's twisted experiment go on like that. I know I've called you a cold-hearted scientist in the past, sis. But you're nowhere near as bad as Dr. Fuji was. You really care about people and Pokemon, but he only saw Amber and Zwei as lab experiments he could toy with… like they weren't even living beings."

Diane nodded. "And so ultimately, the fault in everything that happened lies with him. Maybe you could've changed what happened, then again maybe you couldn't have. In the end, Amber and Zwei turned out the way they did because Dr. Fuji didn't respect them as living beings."

"I guess I should probably just be happy I survived this whole thing." Dawn replied. "This whole thing really has me shaken up."

"Dawn, perhaps you should come with Cynthia and I to Cyllage City." Diane suggested. "I'm sure it's on the way to your next contest. Besides, you could probably use the company right now."

"Thanks, but are you sure Cynthia won't mind if I tag along with you?" Dawn asked.

"I'm sure she'll be fine with it once I explain the situation." Diane assured her. "Of course… if you are going to be traveling with us for a while, there's something you should probably know."

"What's that?" Dawn asked.

Diane took a deep breath. "Cynthia and I are lovers."

Dawn's eyes widened in surprise upon hearing this news. "Uh… that's great! Good for you, sis. So does mom know?"

"Not yet. I'm working up the courage to tell her." Diane answered. "Surprisingly, I'm a little more worried about what mom will think of the age difference. Cynthia is a bit older than me, after all."

"Well, I'm happy for you Diane." Dawn assured her. "I've always thought you could use, uh… someone like that in your life."

"I'm really glad you don't have a problem with this Dawn." Cynthia told her. "Well, we should probably meet up with Cynthia and explain the situation."

With that, the sisters got up from the couch. A few seconds after Diane started to head for the elevator, she soon noticed that Dawn wasn't following her.

Diane turned back to see what the problem was. "What's wrong?"

"I was just thinking… Amber and Drei are still out there." Dawn explained. "Who knows what they'll end up doing?"

"I'm sure this Lysandre you told me about will find some way to stop them." Diane assumed.

"I'm not so sure about that." Dawn told her. "Zwei was able to take down Palkia. I don't know how Lysandre expects to stop them. Amber and Zwei could probably destroy the whole world if they wanted to, and they could show up at anytime or anyplace to do it. Who knows where they'll show up?"

* * *

It was midafternoon in Mauville City as Megan Lewis prepared to go out. The white-haired nineteen-year-old wheeled herself over to the full-length mirror in her room to get a good look at her appearance. The light-green dress she had chosen to wear looked okay, but she still sighed when she saw herself in her wheelchair. The chair was something that Megan was still getting used to, as she had only been in the thing for less than a year. It was still a major adjustment for her, though one that was not quite as hard as dealing with the incident that had put Megan in the chair in the first place.

Several months ago Megan was just an ordinary girl living in the Mauville Hills apartment complex of the city. Her grades in school were perfect and it seemed like she had a bright future ahead of her. Then one day as she was walking home from school, some goon hiding in an alley grabbed her and knocked her out with something. When Megan woke up later, she had no memory of whom she was and had been dressed in a Team Rocket uniform. It had seemed that the infamous criminal organization from Kanto had abducted her and other young people around her age and had brainwashed them to become soldiers for their cause.

At the time, Megan had simply decided to accept her fate, as horrible as it was. It had seemed her old life had been lost forever along with her name. All she had at the time was the designation that Team Rocket had given her, Recruit 53. Then one day Megan and another brainwashed recruit had been ordered to recapture one of their fellow soldiers who had somehow managed to escape, a redheaded young man she only knew as Recruit 17. Right when they had cornered 17, Megan felt something burrowing into her mind. Images from her past flashed had before her and the next thing she knew she was unconscious.

Megan had awakened days later in a hospital in Saffron City with her memories fully restored, but whatever had happened to her had left her with brain damage. Megan had been unable to move her legs and her left arm ever since the incident. Though all things considered, she realized she was still much better of than the soldier who had gone with her on that mission, a young man she had only known as Recruit 30. Whatever it was that had unlocked her memories and caused her brain damage had apparently happened to him as well. As far as Megan knew, the young man formerly known as Recruit 30 was still in a coma.

Megan was shaken from her thoughts by the sound of someone running into her room. The person in question was a twelve-year-old boy with dark-brown hair and lavender eyes like Megan's. He had on a black shirt and a green jacket with short sleeves and tan shorts. The boy in question was Megan's little brother, Patrick. Patrick was Pokemon Trainer who had been on his journey since before Megan's abduction and had participated in both the Hoenn and Sinnoh League competitions. He had come back to the city for one special reason.

"C'mon sis! The big Pokemon Trade Meet has already started!" Patrick told her. "If we wait too long, it'll be over."

"Okay, okay. I'm coming." Megan told him. "Of course I don't seem like I have to go with you to this thing. It's not like you need supervision, and I have no plans to trade my Kirlia."

"I know. But I don't get to spend much time with you anymore, sis." Patrick pointed out. "Besides, mom thinks you should start getting out of the house more."

At this, Megan let out a heavy sigh. She had to admit that her mother had a point. Ever since she returned home, Megan had started to become something of a recluse.

"Okay. Let's go out so I can watch you trade Pokemon." Megan decided.

With that, Megan and Patrick left the apartment complex and ventured into the indoor metropolis that was Mauville City. Within a few minutes, the two had made it to the park where the city was holding it's annual Pokemon Trade Meet. The Meet was a yearly event where Pokemon Trainers from all over the world would flock together and trade some of the Pokemon they had collected. It was a good way for some trainers to get Pokemon that they normally wouldn't find at all in their home region. By the time Patrick and Megan arrived, the park was already teeming with trainers of all ages.

Not long after they arrived, Megan and Patrick spotted a young woman in her early twenties with long green hair that had a slight curl to it. She had on black sunglasses styled like a visor and a long black coat with fingerless black gloves. The young woman was merely standing in the middle of the park watching everyone.

"I don't know who she is, but she looks way cool." Patrick declared with a look of awe.

"She certainly is exotic-looking." Megan admitted.

Suddenly Patrick ran up to the mysterious woman. The green-haired stranger turned upon noticing him, and it was then that Megan could see that she had on a distinct metal chocker with a Keystone embedded into the front.

"Excuse me! Do you have any Pokemon from the Kalos Region?" Patrick asked the stranger. "If you do, I'm willing to trade you my Porygon2 for it. It's a shiny."

"…Porygon2?" the green-haired woman repeated. "That's an artificial Pokemon. You're truly willing to trade it?"

"Yep. Actually, it originally belonged to my sister." Patrick revealed as Megan wheeled her chair closer. "She got it when it was just a Porygon, but when she traded it to me she had it hold an Up-Grade so it could evolve. I gotta warn you though, it's not that strong a Pokemon. Certainly not as strong as the Metang she traded me."

"I see. So because this Porygon2 does not live up to your standards, you choose to discard it." The stranger observed. "Does its life mean that little to you because it is artificial?"

"Huh?" Patrick spoke with a raised eyebrow.

The green-haired woman shook her head and pulled an ordinary pokeball from her coat pocket. "This is a Pumpkaboo that I captured not long ago, a Ghost Pokemon from the Kalos Region. Will that be an acceptable trade?"

"Whoa! You bet!" Patrick answered. "I'm Patrick, by the way. This here is my sister, Megan. Mind if we get your name?"

"…Amber Drei." The stranger answered. "I believe that trade machine over there is available."

Megan followed after Amber and Patrick and watched as they made the trade. The transaction was completed in a matter of seconds.

"There ya go." Patrick spoke as he shook Amber's hand. "Two things you should know about that Pokemon though. First, I had it hold a Dubious Disk that a friend of mine found for me before we traded it, so now that Porygon2 will evolve into a Porygon-Z. No need to thank me. Anyway, the second thing is that its nickname is Tron."

"Tron?" Amber repeated with a raised eyebrow. "How did you come up with such a name?"

"Ask my sister." Patrick replied. "She's the one who gave it that name."

Megan saw that Amber was looking straight at her. "I guess it was the best nickname that fit when I saw Tron. I mean Porygon all seem like something out of a sci-fi movie."

"Because they were artificially created?" Amber asked.

"Well… yeah. I always thought that was a little weird." Megan admitted. "I don't know whose idea it was to issue a Pokemon like that to me."

"Issue it?" Amber repeated. "Explain."

At this point, Megan realized that she had said a little too much. "Uh… that's kind of a long story."

Amber grabbed hold of Megan's shoulder. "You will show me."

Suddenly it seemed to Megan like Amber's eyes were glowing from behind her sunglasses. The next thing Megan knew, it seemed like something was burrowing into her mind, just like what happened when she had cornered Recruit 17. Megan could do nothing as she saw images of her time as Recruit 53 replayed in her head. One series of images seemed to replay over and over again several times like a video on a loop. The images were of a mission she and Recruit 17 had gone on one night with their commander, a man Megan had only known as Carson.

The three had gone out to raid a warehouse in Saffron City. During the raid, they had encountered a strange Pokemon with glowing blue eyes. Whatever it was, the Pokemon had tossed her and the Pokemon she had around like ragdolls and knocked them out fairly quickly. After these events replayed for what seemed like the twentieth time in the space of only a few seconds, Megan felt an intense pain like an icepick had been shoved into her skull. Whatever was burrowing into her mind seemed to stop and Megan found she was having a major nosebleed.

"You've been very helpful." Amber told her. "Consider the gift I just gave you my thanks." With that, the green-haired stranger calmly walked off.

"Hey! Come back here!" Patrick called. "What the hell did you do to my sister?"

"It's okay, Patrick. Whatever it was, I think I'm okay." Megan told him as she wiped the blood from her face with her wrist.

After wiping the blood though, Megan paused. She realized she had just wiped away the blood with her left wrist. The white-haired girl moved her left arm around a bit to make sure it was working. Megan then managed to move her knees.

Patrick's jaw was hanging open in total shock. "Sis! You can move your arm and legs?"

"How… how is the possible?" a stunned Megan asked. "Who was that woman?"

* * *

Amber had only gotten a few feet away from the giant square building that was Mauville City before stopping on the side of the road. The green-haired clone reached into her pocket and threw out Zwei's pokeball. The psychic feline burst out of the ball and hovered in the air before her.

"Was that Pokemon Trade Meet interesting, Amber?" Zwei asked.

"It was more than interesting." Amber revealed as she pulled out Tron's ball. "I traded that Pumpkaboo we captured for a Pokemon similar to us. Time to meet our new partner."

Flying out of the ball that Amber threw into the air was an almost duck-like Pokemon with a smooth body. It was mainly electric blue with large eyes and a slender neck. Its long smooth beak was light blue, as was its underside. On the sides of its body rather than wings was a pair of light blue ovular attachments, and attached to its rear was a light blue balloon-like tail. Only a second after the Pokemon emerged however, its body glowed with a white light and it changed shape. The light cleared and the digital life form became more like a humming bird, with the attachments on the sides of its torso now more like wings. Its neck had detached from its body, allowing its head to turn upside-down. Its eyes had also become yellow, very large and somehow crazed.

Amber removed her visor and looked her new Pokemon in the eye. _'Hello Tron, I'm your new trainer. Your previous trainer traded you because he thought you were too ineffective in battle. Can you hear my thoughts?'_

 _'…Affirmative.'_ A mechanical voice responded in Amber's head. _'It is a pleasure to meet, meet, meet you.'_

"Why did it repeat itself just now?" Zwei asked with a quirked brow.

"The update software that allows a Porygon2 to evolve into Porygon-Z is corrupted." Amber explained out loud. "As a result, Porygon-Z are known to behave eratically."

 _'Query: How did my original trainer feel about her brother trading me?'_ Tron's voice asked in Amber's head. _'Did she POLKA have any objections?'_

"Your original trainer didn't object." Amber told it. "In fact she seems to think your entire species is strange. Tell me something, Tron. Did you ever wonder why humans created you and your kind?"

 _'Response: I must admit that I LIKE TOAST that I never thought about such things before.'_ Tron answered. _'From what you have just told me though… I can only conclude that my former trainers never saw me as anything more than an object.'_

"I can assure you that I don't see you that way." Amber told the digital Pokemon. "The fact is that you are no different from Zwei and myself. The three of us were all created through artificial means. We are products of science who have no place in this world."

"What shall we do now, Amber?" Zwei asked.

"We shall find other Pokemon who are like us." Amber decided. "Including the original Mewtwo. Then, once we do, we shall remake this world."

"How do you suggest we find Mewtwo Ein?" Zwei asked.

"Tron's original trainer encountered him in the past." Amber revealed. "I scanned her mind and found that she encountered him twice in Saffron City in Kanto. I don't know if the first Mewtwo can still be found there, but it's a place to start looking."

"But will he join us?" Zwei asked.

"It might take a little convincing, but I believe he will." Amber answered. "Even if we have to use force."

MEWTWO ZWEI – END

* * *

 **Afterward:** That concludes the latest story in my Pokemon AU. Sorry if anyone reading found it too short, but after doing a big multi-chapter story like the Yu-Gi-Oh! ZEXAL story I just did, I find that I like to work on projects that are a little simpler. In any case, I hope everyone enjoyed this little tale. I certainly had a blast writing. One thing I can assure everyone though is that Amber Drei and Zwei will show up in this AU again. I haven't figured out a lot of the major details yet, but I'm thinking that there will be at least two more major stories involving these characters. One of those stories might also involve that new mechanical Pokemon Magearna, but nothing has been decided yet.

In the meantime, I think I'm going to go back to work on my _Thunder in Kanto_ story, which I know I've neglected for far too long. So until next time, thanks to everyone who read and enjoyed this story.

Please review and let me know what you think.


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